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{ "count": 373, "next": "?page=2", "previous": null, "list": [ { "name": "BRENDA", "description": "Internationally leading information system on all aspects of enzymes, including function, structure, involvement in diseases, application, engineering, and molecular properties. The database includes hundreds of milllions of enzyme data and is compiled from manual literature annotation, data integration from other databases and predicted enzyme functions and locations.", "homepage": "http://www.brenda-enzymes.org", "biotoolsID": "brenda", "biotoolsCURIE": "biotools:brenda", "version": [], "otherID": [], "relation": [ { "biotoolsID": "bto", "type": "includes" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" }, { "uri": "http://edamontology.org/operation_3194", "term": "Genome feature comparison" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0305", "term": "Literature search" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" }, { "uri": "http://edamontology.org/operation_0269", "term": "Transmembrane protein prediction" }, { "uri": "http://edamontology.org/operation_2241", "term": "Transmembrane protein visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0990", "term": "Compound name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2342", "term": "Pathway or network name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2365", "term": "Pathway or network accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1187", "term": "PubMed ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1179", "term": "NCBI taxonomy ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1051", "term": "Ontology name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1012", "term": "Enzyme name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1011", "term": "EC number" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2024", "term": "Enzyme kinetics data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2342", "term": "Pathway or network name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2365", "term": "Pathway or network accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1046", "term": "Strain name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2909", "term": "Organism name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1179", "term": "NCBI taxonomy ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1039", "term": "SCOP domain identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2700", "term": "CATH identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1012", "term": "Enzyme name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1011", "term": "EC number" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2024", "term": "Enzyme kinetics data" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "de.NBI", "DSMZ Digital Diversity" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Data", "Tools", "Interoperability" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.dsmz.de/", "type": [ "Other" ], "note": null }, { "url": "https://hub.dsmz.de/#/", "type": [ "Service" ], "note": null }, { "url": "https://www.brenda-enzymes.org/", "type": [ "Service" ], "note": null }, { "url": "https://brenda-enzymes.org/support.php", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.brenda-enzymes.org/copy.php", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.brenda-enzymes.org/introduction.php", "type": [ "Citation instructions" ], "note": null }, { "url": "https://www.brenda-enzymes.org/tutorial.php", "type": [ "Training material" ], "note": null }, { "url": "https://www.brenda-enzymes.org/help.php", "type": [ "Training material" ], "note": null }, { "url": "https://www.brenda-enzymes.org/faq.php", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa1025", "pmid": "33211880", "pmcid": "PMC7779020", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BRENDA, the ELIXIR core data resource in 2021: New developments and updates", "abstract": "The BRENDA enzyme database (https://www.brendaenzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, lig- and information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.", "date": "2021-01-08T00:00:00Z", "citationCount": 393, "authors": [ { "name": "Chang A." }, { "name": "Jeske L." }, { "name": "Ulbrich S." }, { "name": "Hofmann J." }, { "name": "Koblitz J." }, { "name": "Schomburg I." }, { "name": "Neumann-Schaal M." }, { "name": "Jahn D." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gky1048", "pmid": "30395242", "pmcid": "PMC6323942", "type": [], "version": null, "note": null, "metadata": { "title": "BRENDA in 2019: A European ELIXIR core data resource", "abstract": "The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system. The core database provides a comprehensive overview on enzymes. A collection of 4.3 million data for ∼84 000 enzymes manually evaluated and extracted from ∼140 000 primary literature references is combined with information obtained by text and data mining, data integration and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, predicted enzyme locations and genome annotations. Major developments are a revised ligand summary page and the structure search now including a similarity and isomer search. BKMS-react, an integrated database containing known enzyme-catalyzed reactions, is supplemented with further reactions and improved access to pathway connections. In addition to existing enzyme word maps with graphical information of enzyme specific terms, plant word maps have been developed. They show a graphical overview of terms, e.g. enzyme or plant pathogen information, connected to specific plants. An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented. Based on a decision by the IUBMB enzyme task force the enzyme class EC 7 has been established for 'translocases-, enzymes that catalyze a transport of ions or metabolites across cellular membranes.", "date": "2019-01-08T00:00:00Z", "citationCount": 296, "authors": [ { "name": "Jeske L." }, { "name": "Placzek S." }, { "name": "Schomburg I." }, { "name": "Chang A." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1016/j.jbiotec.2017.04.020", "pmid": "28438579", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The BRENDA enzyme information system–From a database to an expert system", "abstract": "Enzymes, representing the largest and by far most complex group of proteins, play an essential role in all processes of life, including metabolism, gene expression, cell division, the immune system, and others. Their function, also connected to most diseases or stress control makes them interesting targets for research and applications in biotechnology, medical treatments, or diagnosis. Their functional parameters and other properties are collected, integrated, and made available to the scientific community in the BRaunschweig ENzyme DAtabase (BRENDA). In the last 30 years BRENDA has developed into one of the most highly used biological databases worldwide. The data contents, the process of data acquisition, data integration and control, the ways to access the data, and visualizations provided by the website are described and discussed.", "date": "2017-11-10T00:00:00Z", "citationCount": 133, "authors": [ { "name": "Schomburg I." }, { "name": "Jeske L." }, { "name": "Ulbrich M." }, { "name": "Placzek S." }, { "name": "Chang A." }, { "name": "Schomburg D." } ], "journal": "Journal of Biotechnology" } }, { "doi": "10.1093/nar/gku1068", "pmid": "25378310", "pmcid": "PMC4383907", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA in 2015: Exciting developments in its 25th year of existence", "abstract": "The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text and data mining, data integration, and prediction algorithms. Approximately 300 million data include enzyme function and molecular data from more than 30 000 organisms. The manually derived core contains 3 million data from 77 000 enzymes annotated from 135 000 literature references. Each entry is connected to the literature reference and the source organism. They are complemented by information on occurrence, enzyme/disease relationships from text mining, sequences and 3D structures from other databases, and predicted enzyme location and genome annotation. Functional and structural data of more than 190 000 enzyme ligands are stored in BRENDA. New features improving the functionality and analysis tools were implemented. The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data. Word Maps for enzymes obtained from PubMed.", "date": "2015-01-28T00:00:00Z", "citationCount": 161, "authors": [ { "name": "Chang A." }, { "name": "Schomburg I." }, { "name": "Placzek S." }, { "name": "Jeske L." }, { "name": "Ulbrich M." }, { "name": "Xiao M." }, { "name": "Sensen C.W." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkn820", "pmid": "18984617", "pmcid": "PMC2686525", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA, AMENDA and FRENDA the enzyme information system: New content and tools in 2009", "abstract": "The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties. The database covers information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure and stability, mutants and enzyme engineering, preparation and isolation, the application of enzymes, and ligand-related data. The data in BRENDA are manually curated from more than 79 000 primary literature references. Each entry is clearly linked to a literature reference, the origin organism and, where available, to the protein sequence of the enzyme protein. A new search option provides the access to protein-specific data. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are additional databases created by continuously improved text-mining procedures. These databases ought to provide a complete survey on enzyme data of the literature collection of PubMed. The web service via a SOAP (Simple Object Access Protocol) interface for access to the BRENDA data has been further enhanced. © 2008 The Author(s).", "date": "2009-01-09T00:00:00Z", "citationCount": 314, "authors": [ { "name": "Chang A." }, { "name": "Scheer M." }, { "name": "Grote A." }, { "name": "Schomburg I." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkq1089", "pmid": "21062828", "pmcid": "PMC3013686", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA, the enzyme information system in 2011", "abstract": "The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references increased by 30% to more than 100 000, the number of ligand structures by 45% to almost 100 000. New query, analysis and data management tools were implemented to improve data processing, data presentation, data input and data access. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. The disease text mining part is strongly enhanced. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology. A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models. © The Author(s) 2010.", "date": "2011-01-01T00:00:00Z", "citationCount": 353, "authors": [ { "name": "Scheer M." }, { "name": "Grote A." }, { "name": "Chang A." }, { "name": "Schomburg I." }, { "name": "Munaretto C." }, { "name": "Rother M." }, { "name": "Sohngen C." }, { "name": "Stelzer M." }, { "name": "Thiele J." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1186/1471-2105-12-329", "pmid": "21827651", "pmcid": "PMC3166944", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Development of a classification scheme for disease-related enzyme information", "abstract": "Background: BRENDA (BRaunschweig ENzyme DAtabase, http://www.brenda-enzymes.org) is a major resource for enzyme related information. First and foremost, it provides data which are manually curated from the primary literature. DRENDA (Disease RElated ENzyme information DAtabase) complements BRENDA with a focus on the automatic search and categorization of enzyme and disease related information from title and abstracts of primary publications. In a two-step procedure DRENDA makes use of text mining and machine learning methods.Results: Currently enzyme and disease related references are biannually updated as part of the standard BRENDA update. 910,897 relations of EC-numbers and diseases were extracted from titles or abstracts and are included in the second release in 2010. The enzyme and disease entity recognition has been successfully enhanced by a further relation classification via machine learning. The classification step has been evaluated by a 5-fold cross validation and achieves an F1 score between 0.802 ± 0.032 and 0.738 ± 0.033 depending on the categories and pre-processing procedures. In the eventual DRENDA content every category reaches a classification specificity of at least 96.7% and a precision that ranges from 86-98% in the highest confidence level, and 64-83% for the smallest confidence level associated with higher recall.Conclusions: The DRENDA processing chain analyses PubMed, locates references with disease-related information on enzymes and categorises their focus according to the categories causal interaction, therapeutic application, diagnostic usage and ongoing research. The categorisation gives an impression on the focus of the located references. Thus, the relation categorisation can facilitate orientation within the rapidly growing number of references with impact on diseases and enzymes. The DRENDA information is available as additional information in BRENDA. © 2011 Söhngen et al; licensee BioMed Central Ltd.", "date": "2011-08-09T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Sohngen C." }, { "name": "Chang A." }, { "name": "Schomburg D." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1093/nar/gkh081", "pmid": "14681450", "pmcid": "PMC308815", "type": [ "Other" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gks1049", "pmid": "23203881", "pmcid": "PMC3531171", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in BRENDA", "abstract": "The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases. BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism. Enzyme ligands are stored with their structures and can be accessed via their names, synonyms or via a structure search. FRENDA (Full Reference ENzyme DAta) and AMENDA (Automatic Mining of ENzyme DAta) are based on text mining methods and represent a complete survey of PubMed abstracts with information on enzymes in different organisms, tissues or organelles. The supplemental database DRENDA provides more than 910000 new EC number-disease relations in more than 510 000 references from automatic search and a classification of enzyme-disease-related information. KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts. The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes. The biochemical reaction database BKM-react contains non-redundant enzyme-catalysed and spontaneous reactions and was developed to facilitate and accelerate the construction of biochemical models. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 347, "authors": [ { "name": "Schomburg I." }, { "name": "Chang A." }, { "name": "Placzek S." }, { "name": "Sohngen C." }, { "name": "Rother M." }, { "name": "Lang M." }, { "name": "Munaretto C." }, { "name": "Ulas S." }, { "name": "Stelzer M." }, { "name": "Grote A." }, { "name": "Scheer M." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1016/s0968-0004(01)02027-8", "pmid": "11796225", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA: A resource for enzyme data and metabolic information", "abstract": "BRENDA (BRaunschweig ENzyme DAtabase), founded in 1987 by Dietmar Schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme -ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism. BRENDA is accessible free of charge to the academic community at http://www.brenda.uni-koeln.de/; commercial users need a license available from http://www.science-factory.com/.", "date": "2002-01-01T00:00:00Z", "citationCount": 159, "authors": [ { "name": "Schomburg I." }, { "name": "Chang A." }, { "name": "Hofmann O." }, { "name": "Ebeling C." }, { "name": "Ehrentreich F." }, { "name": "Schomburg D." } ], "journal": "Trends in Biochemical Sciences" } }, { "doi": "10.1093/nar/gkl972", "pmid": "17202167", "pmcid": "PMC1899097", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA, AMENDA and FRENDA: The enzyme information system in 2007", "abstract": "The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.de) is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzyme's source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007. © 2007 Oxford University Press.", "date": "2007-01-01T00:00:00Z", "citationCount": 137, "authors": [ { "name": "Barthelmes J." }, { "name": "Ebeling C." }, { "name": "Chang A." }, { "name": "Schomburg I." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/30.1.47", "pmid": "11752250", "pmcid": "PMC99121", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "BRENDA, enzyme data and metabolic information", "abstract": "BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, classified in approximately 3900 EC numbers. BRENDA is an important tool for biochemical and medical research covering information on properties of all classified enzymes, including data on the occurrence, catalyzed reaction, kinetics, substrates/products, inhibitors, cofactors, activators, structure and stability. All data are connected to literature references which in turn are linked to PubMed. The data and information provide a fundamental tool for research of enzyme mechanisms, metabolic pathways, the evolution of metabolism and, furthermore, for medicinal diagnostics and pharmaceutical research. The database is a resource for data of enzymes, classified according to the EC system of the IUBMB Enzyme Nomenclature Committee, and the entries are cross-referenced to other databases, i.e. organism classification, protein sequence, protein structure and literature references. BRENDA provides an academic web access at http://www.brenda.uni-koeln.de.", "date": "2002-01-01T00:00:00Z", "citationCount": 384, "authors": [ { "name": "Schomburg I." }, { "name": "Chang A." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkq968", "pmid": "21030441", "pmcid": "PMC3013802", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "The BRENDA Tissue Ontology (BTO): The first all-integrating ontology of all organisms for enzyme sources", "abstract": "BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms. The project started in 2003 to create a connection between the enzyme data collection of the BRENDA enzyme database and a structured network of source tissues and cell types. Currently, BTO contains more than 4600 different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. The content of the ontology is constantly curated with ̃1000 new terms each year. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues. Important areas of applications of the BTO terms are the detection of enzymes in tissues and the provision of a solid basis for text-mining approaches in this field. It is widely used by lab scientists, curators of genomic and biochemical databases and bioinformaticians. 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A gene regulatory network (GRN) consists of genes, transcription factors, and the regulatory connections between them which govern the level of expression of mRNA and protein from genes. The original motivation came from our efforts to perform parameter estimation and forward simulation of the dynamics of a differential equations model of a small GRN with 21 nodes and 31 edges. We wanted a quick and easy way to visualize the weight parameters from the model which represent the direction and magnitude of the influence of a transcription factor on its target gene, so we created GRNsight. GRNsight automatically lays out either an unweighted or weighted network graph based on an Excel spreadsheet containing an adjacency matrix where regulators are named in the columns and target genes in the rows, a Simple Interaction Format (SIF) text file, or a GraphML XML file. When a user uploads an input file specifying an unweighted network, GRNsight automatically lays out the graph using black lines and pointed arrowheads. For a weighted network, GRNsight uses pointed and blunt arrowheads, and colors the edges and adjusts their thicknesses based on the sign (positive for activation or negative for repression) and magnitude of the weight parameter. GRNsight is written in JavaScript, with diagrams facilitated by D3.js, a data visualization library. Node.js and the Express framework handle server-side functions. GRNsight's diagrams are based on D3.js's force graph layout algorithm, which was then extensively customized to support the specific needs of GRNs. Nodes are rectangular and support gene labels of up to 12 characters. The edges are arcs, which become straight lines when the nodes are close together. Self-regulatory edges are indicated by a loop.When a user mouses over an edge, the numerical value of the weight parameter is displayed. Visualizations can be modified by sliders that adjust the force graph layout parameters and through manual node dragging. GRNsight is best-suited for visualizing networks of fewer than 35 nodes and 70 edges, although it accepts networks of up to 75 nodes or 150 edges. GRNsight has general applicability for displaying any small, unweighted or weighted network with directed edges for systems biology or other application domains. GRNsight serves as an example of following and teaching best practices for scientific computing and complying with FAIR principles, using an open and test-driven development model with rigorous documentation of requirements and issues on GitHub. An exhaustive unit testing framework using Mocha and the Chai assertion library consists of around 160 automated unit tests that examine nearly 530 test files to ensure that the program is running as expected. 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These data have the potential to unravel the complexity of epigenomic regulation. However, their effective use is hindered by the lack of flexible and easy-to-use methods for data retrieval. Extracting region sets of interest is a cumbersome task that involves several manual steps: identifying the relevant experiments, downloading the corresponding data files and filtering the region sets of interest. Here we present the DeepBlue Epigenomic Data Server, which streamlines epigenomic data analysis as well as software development. DeepBlue provides a comprehensive programmatic interface for finding, selecting, filtering, summarizing and downloading region sets. It contains data from four major epigenome projects, namely ENCODE, ROADMAP, BLUEPRINT and DEEP. DeepBlue comes with a user manual, examples and a well-documented application programming interface (API). The latter is accessed via the XML-RPC protocol supported by many programming languages. 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[], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://pdestrian.vu-compmedchem.nl/faq.php", "type": [ "Citation instructions", "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jmedchem.5b01813", "pmid": "26908025", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PDEStrIAn: A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design", "abstract": "A systematic analysis is presented of the 220 phosphodiesterase (PDE) catalytic domain crystal structures present in the Protein Data Bank (PDB) with a focus on PDE-ligand interactions. The consistent structural alignment of 57 PDE ligand binding site residues enables the systematic analysis of PDE-ligand interaction fingerprints (IFPs), the identification of subtype-specific PDE-ligand interaction features, and the classification of ligands according to their binding modes. We illustrate how systematic mining of this phosphodiesterase structure and ligand interaction annotated (PDEStrIAn) database provides new insights into how conserved and selective PDE interaction hot spots can accommodate the large diversity of chemical scaffolds in PDE ligands. A substructure analysis of the cocrystallized PDE ligands in combination with those in the ChEMBL database provides a toolbox for scaffold hopping and ligand design. These analyses lead to an improved understanding of the structural requirements of PDE binding that will be useful in future drug discovery studies.", "date": "2016-08-11T00:00:00Z", "citationCount": 56, "authors": [ { "name": "Jansen C." }, { "name": "Kooistra A.J." }, { "name": "Kanev G.K." }, { "name": "Leurs R." }, { "name": "De Esch I.J.P." }, { "name": "De Graaf C." } ], "journal": "Journal of Medicinal Chemistry" } } ], "credit": [ { "name": "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Chris de Graaf", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Georgi K. 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Its key function is to provide users with predictions about the interactions that their entities of interest (proteins or small molecules) may be making with other such entities, and to visualise where a set of entities of interest can be found within the STITCH network. Direct traceable links to the original sources on which interactions are described in the network, make it easy for users to trace the provenance of the data.", "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://stitch.embl.de/cgi/show_info_page.pl?UserId=pRfi11Qlkhnx&sessionId=sEfmbh_T7QLq", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkm795", "pmid": "18084021", "pmcid": "PMC2238848", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "STITCH: Interaction networks of chemicals and proteins", "abstract": "The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH ('search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/. © 2007 The Author(s).", "date": "2008-01-01T00:00:00Z", "citationCount": 754, "authors": [ { "name": "Kuhn M." }, { "name": "von Mering C." }, { "name": "Campillos M." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkp937", "pmid": "19897548", "pmcid": "PMC2808890", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 2: An interaction network database for small molecules and proteins", "abstract": "Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-06T00:00:00Z", "citationCount": 231, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Franceschini A." }, { "name": "Campillos M." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Beyer A." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1207", "pmid": "24293645", "pmcid": "PMC3964996", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 4: Integration of protein-chemical interactions with user data", "abstract": "STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms. Compared with the previous version, the number of high-confidence protein-chemical interactions in human has increased by 45%, to 367 000. In this version, we added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data. For example, a user can now upload a spreadsheet with screening hits to easily check which interactions are already known. To increase the coverage of STITCH, we expanded the text mining to include full-text articles and added a prediction method based on chemical structures. We further changed our scheme for transferring interactions between species to rely on orthology rather than protein similarity. This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 413, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Pletscher-Frankild S." }, { "name": "Blicher T.H." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1011", "pmid": "22075997", "pmcid": "PMC3245073", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 3: Zooming in on protein-chemical interactions", "abstract": "To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 250, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Franceschini A." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "EMBL", "email": null, "url": "http://www.embl.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "SUND-KU", "email": null, "url": "http://healthsciences.ku.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EC FP6", "email": null, "url": "http://ec.europa.eu/research/index.cfm", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BMBF", "email": null, "url": "https://www.bmbf.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBO", "email": null, "url": "http://www.embo.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "CPR", "email": null, "url": "http://www.cpr.ku.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "TUD", "email": null, "url": "http://www.biotec.tu-dresden.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "HD-HuB", "email": null, "url": "https://www.hd-hub.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Michael Kuhn", "email": null, "url": "http://stitch1.embl.de/cgi/show_info_page.pl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Michael Kuhn", "email": null, "url": "http://stitch1.embl.de/cgi/show_info_page.pl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hdhub", "additionDate": "2016-02-17T09:43:56Z", "lastUpdate": "2024-11-25T14:25:13.779770Z", "editPermission": { "type": "group", "authors": [ "larsjuhljensen" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AGCOH", "description": "The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography.", "homepage": "http://atlasgeneticsoncology.org", "biotoolsID": "atlasgeneticsoncology", "biotoolsCURIE": "biotools:atlasgeneticsoncology", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0971", "term": "Article" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Query and retrieval of articles on human Genes, Leukemia, Tumors, Cancer prone diseases and cytogenetic associated abnormailities", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Linux" ], "language": [ "Perl" ], "license": "CC-BY-NC-ND-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://atlasgeneticsoncology.org", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks1082", "pmid": "23161685", "pmcid": "PMC3531131", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Atlas of genetics and cytogenetics in oncology and haematology in 2013", "abstract": "The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology. org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlasare researchers and/orclinicians. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 144, "authors": [ { "name": "Huret J.-L." }, { "name": "Ahmad M." }, { "name": "Arsaban M." }, { "name": "Bernheim A." }, { "name": "Cigna J." }, { "name": "Desangles F." }, { "name": "Guignard J.-C." }, { "name": "Jacquemot-Perbal M.-C." }, { "name": "Labarussias M." }, { "name": "Leberre V." }, { "name": "Malo A." }, { "name": "Morel-Pair C." }, { "name": "Mossafa H." }, { "name": "Potier J.-C." }, { "name": "Texier G." }, { "name": "Viguie F." }, { "name": "Wan-Senon S.Y.C." }, { "name": "Zasadzinski A." }, { "name": "Dessen P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkg126", "pmid": "12520000", "pmcid": "PMC165573", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003", "abstract": "The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical entities in oncology, and cancer-prone diseases, a portal towards genetics/cancer, and teaching materials in genetics. This database is made for and by researchers and clinicians, who are encouraged to contribute. The Atlas is part of the genome project and it participates in research on cancer epidemiology.", "date": "2003-01-01T00:00:00Z", "citationCount": 46, "authors": [ { "name": "Huret J.-L." }, { "name": "Dessen P." }, { "name": "Bernheim A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "JL Huret and P Dessen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "INIST CNRS, Nancy, France", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "see http://atlasgeneticsoncology.org", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "igr.fr", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Jean-Loup Huret", "email": "jlhuret@AtlasGeneticsOncology.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Philippe Dessen", "email": "dessen@igr.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "dessen@igr.fr", "additionDate": "2016-03-02T08:53:57Z", "lastUpdate": "2024-11-25T14:24:12.137448Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GWIPS-viz", "description": "Specialized ribosome profiling (ribo-seq) browser providing free access to the genomic alignments of ribo-seq reads in conjunction with mRNA-seq controls along with relevant annotation tracks. Based on the UCSC Genome Browser, the tool’s ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes while the separate tracks for each ribo-seq study enables cross-study comparisons.", "homepage": "http://gwips.ucc.ie", "biotoolsID": "gwips-viz", "biotoolsCURIE": "biotools:gwips-viz", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://gwips.ucc.ie/index.html", "type": [ "Citation instructions" ], "note": null }, { "url": "http://gwips.ucc.ie/Forum/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt1035", "pmid": "24185699", "pmcid": "PMC3965066", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "GWIPS-viz: Development of a ribo-seq genome browser", "abstract": "We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 178, "authors": [ { "name": "Michel A.M." }, { "name": "Fox G." }, { "name": "M. Kiran A." }, { "name": "De Bo C." }, { "name": "O'Connor P.B.F." }, { "name": "Heaphy S.M." }, { "name": "Mullan J.P.A." }, { "name": "Donohue C.A." }, { "name": "Higgins D.G." }, { "name": "Baranov P.V." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1002/pmic.201400603", "pmid": "25736862", "pmcid": "PMC4832365", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms", "abstract": "The boundaries of protein coding sequences are more difficult to define at the 5′ end than at the 3′ end due to potential multiple translation initiation sites (TISs). Even in the presence of phylogenetic data, the use of sequence information only may not be sufficient for the accurate identification of TISs. Traditional proteomics approaches may also fail because the N-termini of newly synthesized proteins are often processed. Thus ribosome profiling (ribo-seq), producing a snapshot of the ribosome distribution across the entire transcriptome, is an attractive experimental technique for the purpose of TIS location exploration. The GWIPS-viz (Genome Wide Information on Protein Synthesis visualized) browser (http://gwips.ucc.ie) provides free access to the genomic alignments of ribo-seq data and corresponding mRNA-seq data along with relevant annotation tracks. In this brief, we illustrate how GWIPS-viz can be used to explore the ribosome occupancy at the 5′ ends of protein coding genes to assess the activity of AUG and non-AUG TISs responsible for the synthesis of proteoforms with alternative or heterogeneous N-termini. The presence of ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes and the availability of datasets from multiple laboratories permits the assessment of the technical reproducibility of the ribosome densities.", "date": "2015-07-01T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Michel A.M." }, { "name": "Ahern A.M." }, { "name": "Donohue C.A." }, { "name": "Baranov P.V." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "Michel AM, Fox G, M Kiran A, De Bo C, O'Connor PB, Heaphy SM", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "School of Biochemistry & Cell Biology, University College Cork", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Science Foundation Ireland", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ucc.ie", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "gwipsviz@gmail.com", "url": "http://gwips.ucc.ie/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "A.Michel@ucc.ie", "additionDate": "2016-05-24T10:54:36Z", "lastUpdate": "2024-11-25T14:23:59.431472Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GUILDify", "description": "Uses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. These gene products are fed to a species-specific interaction network as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm.", "homepage": "http://sbi.imim.es/web/GUILDify.php", "biotoolsID": "guildify", "biotoolsCURIE": "biotools:guildify", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2339", "term": "Ontology concept name" }, "format": [ { "uri": "http://edamontology.org/format_1963", "term": "UniProtKB format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": "Gene prioritization of genes associated with phenotype and diseases Starting seeds: genes associated with a disease\nor\nKeyword(s) of a phenotype or disease Network of associated proteins and drugs", "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3396", "term": "Systems medicine" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://sbi.imim.es/web/GUILDify.php/doc", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btu092", "pmid": "24532728", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "GUILDify: A web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms", "abstract": "Determining genetic factors underlying various phenotypes is hindered by the involvement of multiple genes acting cooperatively. Over the past years, disease-gene prioritization has been central to identify genes implicated in human disorders. Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases. Such methods exploit the guilt-by-association principle in the protein interaction network to uncover novel disease-gene associations. These methods rely on the proximity of a gene in the network to the genes associated with a phenotype and require a set of initial associations. Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein-protein interaction network where the initial phenotype-gene associations are retrieved via free text search on biological databases. GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts user-specified genes. It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies. © 2014 The Author. Published by Oxford University Press. All rights reserved.", "date": "2014-06-15T00:00:00Z", "citationCount": 34, "authors": [ { "name": "Guney E." }, { "name": "Garcia-Garcia J." }, { "name": "Oliva B." } ], "journal": "Bioinformatics" } }, { "doi": "10.1371/journal.pone.0043557", "pmid": "23028459", "pmcid": "PMC3448640", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Exploiting Protein-Protein Interaction Networks for Genome-Wide Disease-Gene Prioritization", "abstract": "Complex genetic disorders often involve products of multiple genes acting cooperatively. Hence, the pathophenotype is the outcome of the perturbations in the underlying pathways, where gene products cooperate through various mechanisms such as protein-protein interactions. Pinpointing the decisive elements of such disease pathways is still challenging. Over the last years, computational approaches exploiting interaction network topology have been successfully applied to prioritize individual genes involved in diseases. Although linkage intervals provide a list of disease-gene candidates, recent genome-wide studies demonstrate that genes not associated with any known linkage interval may also contribute to the disease phenotype. Network based prioritization methods help highlighting such associations. Still, there is a need for robust methods that capture the interplay among disease-associated genes mediated by the topology of the network. Here, we propose a genome-wide network-based prioritization framework named GUILD. This framework implements four network-based disease-gene prioritization algorithms. We analyze the performance of these algorithms in dozens of disease phenotypes. The algorithms in GUILD are compared to state-of-the-art network topology based algorithms for prioritization of genes. As a proof of principle, we investigate top-ranking genes in Alzheimer's disease (AD), diabetes and AIDS using disease-gene associations from various sources. We show that GUILD is able to significantly highlight disease-gene associations that are not used a priori. Our findings suggest that GUILD helps to identify genes implicated in the pathology of human disorders independent of the loci associated with the disorders. © 2012 Guney, Oliva.", "date": "2012-09-21T00:00:00Z", "citationCount": 90, "authors": [ { "name": "Guney E." }, { "name": "Oliva B." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Emre Guney", "email": "emre.guney@upf.edu", "url": null, "orcidid": "http://orcid.org/0000-0002-3466-6535", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Javier Garcia-Garcia", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0001-9539-2606", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "UPF", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "MICINN/MINECO & FEBS BIO2011-22568", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "upf.edu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "baldo.oliva@upf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "baldo.oliva@upf.edu", "additionDate": "2016-04-22T11:32:13Z", "lastUpdate": "2024-11-25T14:23:54.691568Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ray", "description": "De novoassembly of single genomes and metagenomes. Also analyses microbe abundance and performs taxonomic profiling as well as making gene ontology profiling. It can also compare genomic content between samples.", "homepage": "http://denovoassembler.sourceforge.net", "biotoolsID": "ray", "biotoolsCURIE": "biotools:ray", "version": [ "2.3.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": "GPL-3.0", "collectionID": [ "Debian Med", "CWL", "Animal and Crop Genomics", "CloudBioLinux" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sebhtml/ray", "type": [ "Repository" ], "note": null }, { "url": "http://sebhtml.github.io/Ray.web", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://sebhtml.github.io/Ray.web/download.html", "type": "Source code", "note": null, "version": null }, { "url": "http://sebhtml.github.io/Ray.web/download.html", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://sebhtml.github.io/Ray.web/manual.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/gb-2012-13-12-r122", "pmid": "23259615", "pmcid": "PMC4056372", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Ray Meta: Scalable de novo metagenome assembly and profiling", "abstract": "Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net.", "date": "2012-12-22T00:00:00Z", "citationCount": 463, "authors": [ { "name": "Boisvert S." }, { "name": "Raymond F." }, { "name": "Godzaridis E." }, { "name": "Laviolette F." }, { "name": "Corbeil J." } ], "journal": "Genome Biology" } }, { "doi": "10.1089/cmb.2009.0238", "pmid": "20958248", "pmcid": "PMC3119603", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies", "abstract": "An accurate genome sequence of a desired species is now a pre-requisite for genome research. An important step in obtaining a high-quality genome sequence is to correctly assemble short reads into longer sequences accurately representing contiguous genomic regions. Current sequencing technologies continue to offer increases in throughput, and corresponding reductions in cost and time. Unfortunately, the benefit of obtaining a large number of reads is complicated by sequencing errors, with different biases being observed with each platform. Although software are available to assemble reads for each individual system, no procedure has been proposed for high-quality simultaneous assembly based on reads from a mix of different technologies. In this paper, we describe a parallel short-read assembler, called Ray, which has been developed to assemble reads obtained from a combination of sequencing platforms. We compared its performance to other assemblers on simulated and real datasets. We used a combination of Roche/454 and Illumina reads to assemble three different genomes. We showed that mixing sequencing technologies systematically reduces the number of contigs and the number of errors. Because of its open nature, this new tool will hopefully serve as a basis to develop an assembler that can be of universal utilization (availability: http://deNovoAssembler.sf.Net/). For online Supplementary Material, see www.liebertonline.com. Copyright 2010, Mary Ann Liebert, Inc.", "date": "2010-11-01T00:00:00Z", "citationCount": 425, "authors": [ { "name": "Boisvert S." }, { "name": "Laviolette F." }, { "name": "Corbeil J." } ], "journal": "Journal of Computational Biology" } } ], "credit": [ { "name": "Sébastien Boisvert", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jacques Corbeil", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Élénie Godzaridis", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "François Laviolette", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Frédéric Raymond", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Infectious Diseases Research Center, CHUQ Research Center", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "1065, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Faculty of Medicine, Laval University, 1050, av. de la Médecine, Québec (Québec), G1V 0A6, Canada", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Department of Molecular Medicine, Faculty of Medicine, Laval University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Canadian Institutes of Health Research (CIHR), and other", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "NTNU", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Animesh Sharma", "email": "sharma.animesh@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "NTNU", "additionDate": "2016-03-17T14:52:04Z", "lastUpdate": "2024-11-25T14:23:12.573072Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ontology Lookup Service", "description": "Repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. Users can browse the ontologies through the web interface and programatic access is provided via a RESTful API.", "homepage": "http://www.ebi.ac.uk/ols/", "biotoolsID": "ols", "biotoolsCURIE": "biotools:ols", "version": [ "3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3559", "term": "Ontology visualisation" }, { "uri": "http://edamontology.org/operation_3282", "term": "ID mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "EMBL" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/EBISPOT/OLS/", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://www.ebi.ac.uk/ols/docs/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-7-97", "pmid": "16507094", "pmcid": "PMC1420335", "type": [], "version": null, "note": null, "metadata": { "title": "The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries", "abstract": "Background: With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. Results: The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. Conclusion: The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/. © 2006 Côté et al; licensee BioMed Central Ltd.", "date": "2006-02-28T00:00:00Z", "citationCount": 175, "authors": [ { "name": "Cote R.G." }, { "name": "Jones P." }, { "name": "Apweiler R." }, { "name": "Hermjakob H." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1093/nar/gkn252", "pmid": "18467421", "pmcid": "PMC2447739", "type": [], "version": null, "note": null, "metadata": { "title": "The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.", "abstract": "The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and controlled vocabularies. The volume of data available for querying has more than quadrupled since it went into production and OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries.", "date": "2008-01-01T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Cote R.G." }, { "name": "Jones P." }, { "name": "Martens L." }, { "name": "Apweiler R." }, { "name": "Hermjakob H." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1093/nar/gkq331", "pmid": "20460452", "pmcid": "PMC2896109", "type": [], "version": null, "note": null, "metadata": { "title": "The Ontology Lookup Service: Bigger and better", "abstract": "The Ontology Lookup Service (OLS; http://www.ebi.ac.uk/ols) has been providing several means to query, browse and navigate biomedical ontologies and controlled vocabularies since it first went into production 4 years ago, and usage statistics indicate that it has become a heavily accessed service with millions of hits monthly. The volume of data available for querying has increased 7-fold since its inception. OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements in the data model and loaders, as well as interface enhancements have made the OLS easier to use and capture more annotations from the source data. In addition, newly released software packages now provide easy means to fully integrate OLS functionality in external applications. © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-05-11T00:00:00Z", "citationCount": 102, "authors": [ { "name": "Cote R." }, { "name": "Reisinger F." }, { "name": "Martens L." }, { "name": "Barsnes H." }, { "name": "Vizcaino J.A." }, { "name": "Hermjakob H." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Simon Jupp", "email": null, "url": "https://www.ebi.ac.uk/~jupp/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Samples, Phenotypes and Ontologies Team", "email": null, "url": "http://www.ebi.ac.uk/about/spot-team", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": "http://www.ebi.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Elixir", "email": null, "url": "https://www.elixir-europe.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "CORBEL", "email": null, "url": "http://www.corbel-project.eu/home.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "DIACHRON", "email": null, "url": "http://www.diachron-fp7.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": "http://www.ebi.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BioMedBridges", "email": null, "url": "http://www.biomedbridges.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Documentor" ], "note": null }, { "name": "ebi.ac.uk", "email": null, "url": "http://www.ebi.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "OLS GitHub", "email": null, "url": "https://github.com/EBISPOT/OLS", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "ols-support@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": null, "url": "https://github.com/EBISPOT/OLS", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jupp@ebi.ac.uk", "additionDate": "2016-08-26T11:55:20Z", "lastUpdate": "2024-11-25T14:20:55.319933Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NorsNet", "description": "Identification unstructured loops from sequence.", "homepage": "http://ppopen.informatik.tu-muenchen.de/", "biotoolsID": "norsnet", "biotoolsCURIE": "biotools:norsnet", "version": [ "1.0.16" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0470", "term": "Protein secondary structure prediction (coils)" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "NORSnet is a neural network based method that focuses on the identification of unstructured loops.\n\nNORSnet was trained to distinguish between very long contiguous segments with non-regular secondary structure (NORS regions) and well-folded proteins. NORSnet was trained on predicted information rather than on experimental data. Therefore, it was optimized on a large data, which is not biased by today's experimental means of capturing disorder. Thus, NORSnet reached into regions in sequence space that are not covered by the specialized disorder predictors. One disadvantage of this approach is that it is not optimal for the identification of the \"average\" disordered region. Protein amino-acid sequence in fasta format", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "GPL-2.0", "collectionID": [ "Rostlab tools", "PredictProtein" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://rostlab.org/owiki/index.php/Packages", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://rostlab.org/owiki/index.php/Packages", "type": "Source code", "note": null, "version": null }, { "url": "https://rostlab.org/owiki/index.php/Packages", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://rostlab.org/owiki/index.php/Norsnet", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.0030140", "pmid": "17658943", "pmcid": "PMC1924875", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Natively unstructured loops differ from other loops", "abstract": "Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long unstructured loops are a major part of unstructured regions in molecular networks. © 2007 Schlessinger et al.", "date": "2007-01-01T00:00:00Z", "citationCount": 85, "authors": [ { "name": "Schlessinger A." }, { "name": "Liu J." }, { "name": "Rost B." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Avner Schlessinger", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Burkhard Rost", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Jinfeng Liu", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-0343-8222", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "University of California San Diego", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Columbia University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Grant 2R01-LM07329-01 from the National Library of Medicine", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "RostLab", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "help@predictprotein.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "RostLab", "additionDate": "2015-12-02T16:31:52Z", "lastUpdate": "2024-11-25T14:18:37.601604Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pEffect", "description": "Prediction of type III effector proteins from protein sequence.", "homepage": "https://rostlab.org/services/peffect/", "biotoolsID": "peffect", "biotoolsCURIE": "biotools:peffect", "version": [ "0.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1777", "term": "Protein function prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Prediction of gram-negative bacterial type III effector proteins", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux" ], "language": [ "Java", "Perl" ], "license": "GPL-2.0", "collectionID": [ "Bromberglab tools", "Rostlab tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://rostlab.org/owiki/index.php/Packages", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://rostlab.org/owiki/index.php/Packages", "type": "Source code", "note": null, "version": null }, { "url": "https://rostlab.org/owiki/index.php/Packages", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://rostlab.org/owiki/index.php/PEffect", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/srep34516", "pmid": "27713481", "pmcid": "PMC5054392", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Computational prediction shines light on type III secretion origins", "abstract": "Type III secretion system is a key bacterial symbiosis and pathogenicity mechanism responsible for a variety of infectious diseases, ranging from food-borne illnesses to the bubonic plague. In many Gram-negative bacteria, the type III secretion system transports effector proteins into host cells, converting resources to bacterial advantage. Here we introduce a computational method that identifies type III effectors by combining homology-based inference with de novo predictions, reaching up to 3-fold higher performance than existing tools. Our work reveals that signals for recognition and transport of effectors are distributed over the entire protein sequence instead of being confined to the N-terminus, as was previously thought. Our scan of hundreds of prokaryotic genomes identified previously unknown effectors, suggesting that type III secretion may have evolved prior to the archaea/bacteria split. Crucially, our method performs well for short sequence fragments, facilitating evaluation of microbial communities and rapid identification of bacterial pathogenicity-no genome assembly required.", "date": "2016-10-07T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Goldberg T." }, { "name": "Rost B." }, { "name": "Bromberg Y." } ], "journal": "Scientific Reports" } } ], "credit": [ { "name": "Tatyana Goldberg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Yana Bromberg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Burkhard Rost", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Technical University of Munich", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Rutgers University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Alexander von Humboldt foundation through the German Federal Ministry for Education and Research", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ernst Ludwig Ehrlich Studienwerk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "RostLab", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Support", "email": "localization@rostlab.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": null, "email": "localization@rostlab.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "RostLab", "additionDate": "2015-12-02T18:10:26Z", "lastUpdate": "2024-11-25T14:17:40.306486Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "cropPAL", "description": "A data portal to access the compendium of data on crop protein subcellular locations.", "homepage": "http://crop-pal.org/", "biotoolsID": "croppal", "biotoolsCURIE": "biotools:croppal", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Protein subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://crop-pal.org/", "type": [ "Terms of use" ], "note": null }, { "url": "http://crop-pal.org/Tutorialv1.2.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/pcp/pcv170", "pmid": "26556651", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Finding the subcellular location of barley, wheat, rice and maize proteins: The compendium of crop proteins with annotated locations (cropPAL)", "abstract": "Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight precomputed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.", "date": "2016-01-01T00:00:00Z", "citationCount": 44, "authors": [ { "name": "Hooper C.M." }, { "name": "Castleden I.R." }, { "name": "Aryamanesh N." }, { "name": "Jacoby R.P." }, { "name": "Millar A.H." } ], "journal": "Plant and Cell Physiology" } } ], "credit": [ { "name": "ARC Centre of Excellence in Plant Energy Biology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "The University of Western Australia", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Australian National Data Service", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "unimelb.edu.au", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Australia", "email": null, "url": "http://www.plantenergy.uwa.edu.au/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "griffinp@unimelb.edu.au", "additionDate": "2016-09-02T01:22:58Z", "lastUpdate": "2024-11-25T14:16:23.433559Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SWICZ", "description": "A proteomics web database.", "homepage": "http://proteom.biomed.cas.cz/", "biotoolsID": "swicz", "biotoolsCURIE": "biotools:swicz", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_2531", "term": "Experiment report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "Database of proteomic time series data for streptomyces, caulobacter and neiseria Interactive form interlinked with other resources as NCBI, SwissProt, KEGG", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Windows" ], "language": [ "PHP" ], "license": null, "collectionID": [ "Czech Republic", "ELIXIR-CZ", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [ { "url": "http://proteom.biomed.cas.cz", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://proteom.biomed.cas.cz", "type": "Source code", "note": null, "version": null }, { "url": "http://proteom.biomed.cas.cz", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://proteom.biomed.cas.cz", "type": [ "Terms of use", "Citation instructions" ], "note": null }, { "url": "http://proteom.biomed.cas.cz/strepto_new/experimental_strep.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300559", "pmid": "14625849", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server", "abstract": "Here we present the Swiss-Czech Proteomics Server (SWICZ), which hosts the proteomic database summarizing information about the cell cycle of the aquatic bacterium Caulobacter crescentus. The database provides a searchable tool for easy access of global protein synthesis and protein stability data as examined during the C. crescentus cell cycle. Protein synthesis data collected from five different cell cycle stages were determined for each protein spot as a relative value of the total amount of [35S]methionine incorporation. Protein stability of pulse-labeled extracts were measured during a chase period equivalent to one cell cycle unit. Quantitative information for individual proteins together with descriptive data such as protein identities, apparent molecular masses and isoelectric points, were combined with information on protein function, genomic context, and the cell cycle stage, and were then assembled in a relational data-base with a world wide web interface (http://proteom.biomed.cas.cz), which allows the database records to be searched and displays the recovered information. A total of 1250 protein spots were reproducibly detected on two-dimensional gel electropherograms, 295 of which were identified by mass spectroscopy. The database is accessible either through clickable two-dimensional gel electrophoretic maps or by means of a set of dedicated search engines. Basic characterization of the experimental procedures, data processing, and a comprehensive description of the web site are presented. In its current state, the SWICZ proteome database provides a platform for the incorporation of new data emerging from extended functional studies on the C. crescentus proteome.", "date": "2003-10-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Vohradsky J." }, { "name": "Janda I." }, { "name": "Grunenfelder B." }, { "name": "Berndt P." }, { "name": "Roder D." }, { "name": "Langen H." }, { "name": "Weiser J." }, { "name": "Jenal U." } ], "journal": "Proteomics" } }, { "doi": "10.1002/pmic.200500206", "pmid": "16400688", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions", "abstract": "Gene expression databases, acquired by proteomics and transcriptomics, describe physiological and developmental programs at the systems level. Here we analyze proteosynthetic profiles in a bacterium undergoing defined metabolic changes. Streptomyces coelicolor cultured in a defined liquid medium displays four distinct patterns of gene expression associated with growth on glutamate, diauxic transition, and growth on maltose and ammonia that terminates by starvation for nitrogen and entry into stationary phase. Principal component and fuzzy duster analyses of the proteome database of 935 protein spot profiles revealed principal kinetic patterns. Online linkage of the proteome database (SWICZ) to a protein-function database (KEGG) revealed limited correlations between expression profiles and metabolic pathway activities. Proteins belonging to principal metabolic pathways defined characteristic kinetic profiles correlated with the physiological state of the culture. These analyses supported the concept that metabolic flux was regulated not by individual enzymes but rather by groups of enzymes whose synthesis responded to changes in nutritional conditions. Higher-level regulation is reflected by the distribution of all kinetic profiles into only nine groups. The observation that enzymes representing principal metabolic pathways displayed their own distinctive average kinetic profiles suggested that expression of a \"high-flux backbone\" may dominate regulation of metabolic flux. © 2006 Wiley-VCH Verlag GmbH & Co. KGaA.", "date": "2006-02-01T00:00:00Z", "citationCount": 11, "authors": [ { "name": "Vohradsky J." }, { "name": "Thompson C.J." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "Ivan Janda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jiří Vohradský", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Bobek", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Urs Jenal", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Karel Mikulik", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Marek Basler", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Bjorn Grunenfelder", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Institute of Microbiology, Prague, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Biozentrum, Univ. Basel, Switzerland", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Czech Science Foundation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Jiří Vohradský", "email": "vohr@biomed.cas.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Jiří Vohradský", "email": "vohr@biomed.cas.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2015-11-25T19:40:48Z", "lastUpdate": "2024-11-25T14:10:47.731263Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cocoa Genome Hub", "description": "The Cocoa Genome Hub is an integrated web-based database providing centralized access to the cocoa reference genome sequences and genomic resources.", "homepage": "https://cocoa-genome-hub.southgreen.fr/", "biotoolsID": "Cocoa_Genome_Hub", "biotoolsCURIE": "biotools:Cocoa_Genome_Hub", "version": [], "otherID": [], "relation": [ { "biotoolsID": "southgreen", "type": "includedIn" }, { "biotoolsID": "tripal", "type": "uses" }, { "biotoolsID": "jbrowse", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3184", "term": "Sequence assembly visualisation" }, { "uri": "http://edamontology.org/operation_3559", "term": "Ontology visualisation" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" } ], "operatingSystem": [ "Linux" ], "language": [ "PHP", "JavaScript" ], "license": "GPL-2.0", "collectionID": [ "Genome Hub", "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data", "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://cocoa-genome-hub.southgreen.fr/contact", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://api.tripal.info/api/tripal/3.x", "type": [ "API documentation" ], "note": null }, { "url": "https://cocoa-genome-hub.southgreen.fr/content/terms-service", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1186/s12864-017-4120-9", "pmid": "28915793", "pmcid": "PMC5603072", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The cacao Criollo genome v2.0: An improved version of the genome for genetic and functional genomic studies", "abstract": "Background: Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. Methods: We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. Results: The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Conclusion:Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).", "date": "2017-09-15T00:00:00Z", "citationCount": 65, "authors": [ { "name": "Argout X." }, { "name": "Martin G." }, { "name": "Droc G." }, { "name": "Fouet O." }, { "name": "Labadie K." }, { "name": "Rivals E." }, { "name": "Aury J.M." }, { "name": "Lanaud C." } ], "journal": "BMC Genomics" } }, { "doi": "10.1038/ng.736", "pmid": "21186351", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The genome of Theobroma cacao", "abstract": "We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions. © 2011 Nature America, Inc. All rights reserved.", "date": "2011-01-01T00:00:00Z", "citationCount": 578, "authors": [ { "name": "Argout X." }, { "name": "Salse J." }, { "name": "Aury J.-M." }, { "name": "Guiltinan M.J." }, { "name": "Droc G." }, { "name": "Gouzy J." }, { "name": "Allegre M." }, { "name": "Chaparro C." }, { "name": "Legavre T." }, { "name": "Maximova S.N." }, { "name": "Abrouk M." }, { "name": "Murat F." }, { "name": "Fouet O." }, { "name": "Poulain J." }, { "name": "Ruiz M." }, { "name": "Roguet Y." }, { "name": "Rodier-Goud M." }, { "name": "Barbosa-Neto J.F." }, { "name": "Sabot F." }, { "name": "Kudrna D." }, { "name": "Ammiraju J.S.S." }, { "name": "Schuster S.C." }, { "name": "Carlson J.E." }, { "name": "Sallet E." }, { "name": "Schiex T." }, { "name": "Dievart A." }, { "name": "Kramer M." }, { "name": "Gelley L." }, { "name": "Shi Z." }, { "name": "Berard A." }, { "name": "Viot C." }, { "name": "Boccara M." }, { "name": "Risterucci A.M." }, { "name": "Guignon V." }, { "name": "Sabau X." }, { "name": "Axtell M.J." }, { "name": "Ma Z." }, { "name": "Zhang Y." }, { "name": "Brown S." }, { "name": "Bourge M." }, { "name": "Golser W." }, { "name": "Song X." }, { "name": "Clement D." }, { "name": "Rivallan R." }, { "name": "Tahi M." }, { "name": "Akaza J.M." }, { "name": "Pitollat B." }, { "name": "Gramacho K." }, { "name": "D'Hont A." }, { "name": "Brunel D." }, { "name": "Infante D." }, { "name": "Kebe I." }, { "name": "Costet P." }, { "name": "Wing R." }, { "name": "McCombie W.R." }, { "name": "Guiderdoni E." }, { "name": "Quetier F." }, { "name": "Panaud O." }, { "name": "Wincker P." }, { "name": "Bocs S." }, { "name": "Lanaud C." } ], "journal": "Nature Genetics" } } ], "credit": [ { "name": "Argout", "email": "xavier.argout@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-0100-5511", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Droc", "email": "gaetan.droc@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Lanaud", "email": "claire.lanaud@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-6411-7310", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "CIRAD", "email": null, "url": "https://www.cirad.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Maintainer" ], "note": null }, { "name": "ANR", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "owner": "gdroc", "additionDate": "2019-12-13T14:58:07Z", "lastUpdate": "2024-11-25T14:00:43.154205Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RepeatExplorer", "description": "RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes. It employs graph-based clustering of sequence reads to identify repetitive elements and several additional programs that aid in their annotation and quantification.", "homepage": "http://repeatexplorer.org", "biotoolsID": "repeat_explorer", "biotoolsCURIE": "biotools:repeat_explorer", "version": [ "2.3.7 (Galaxy server)", "0.3.7 (command line)" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0379", "term": "Repeat sequence detection" }, { "uri": "http://edamontology.org/operation_0362", "term": "Genome annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [ { "uri": "http://edamontology.org/format_2310", "term": "FASTA-HTML" } ] } ], "note": "Computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes. The pipeline uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify repetitive elements within analyzed samples User-provided shotgun sequencing data Characterization of repetitive sequences", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0798", "term": "Mobile genetic elements" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "Perl", "Python" ], "license": "GPL-3.0", "collectionID": [ "Czech Republic", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [ { "url": "https://bitbucket.org/petrnovak/repex_tarean", "type": [ "Repository" ], "note": null }, { "url": "https://repeatexplorer-elixir.cerit-sc.cz/", "type": [ "Galaxy service" ], "note": null } ], "download": [ { "url": "https://bitbucket.org/petrnovak/repex_tarean", "type": "Source code", "note": null, "version": null }, { "url": "https://bitbucket.org/petrnovak/repex_tarean", "type": "Binaries", "note": null, "version": null }, { "url": "https://toolshed.g2.bx.psu.edu/view/petr-novak/repeatexplorer2", "type": "Software package", "note": "Galaxy toolshed package", "version": null } ], "documentation": [ { "url": "http://repeatexplorer.org", "type": [ "Terms of use", "Citation instructions", "General", "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-11-378", "pmid": "20633259", "pmcid": "PMC2912890", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data", "abstract": "Background: The investigation of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of higher plant nuclear DNA. Since genome-wide characterization of repetitive elements is complicated by their high abundance and diversity, novel approaches based on massively-parallel sequencing are being adapted to facilitate the analysis. It has recently been demonstrated that the low-pass genome sequencing provided by a single 454 sequencing reaction is sufficient to capture information about all major repeat families, thus providing the opportunity for efficient repeat investigation in a wide range of species. However, the development of appropriate data mining tools is required in order to fully utilize this sequencing data for repeat characterization.Results: We adapted a graph-based approach for similarity-based partitioning of whole genome 454 sequence reads in order to build clusters made of the reads derived from individual repeat families. The information about cluster sizes was utilized for assessing the proportion and composition of repeats in the genomes of two model species, Pisum sativum and Glycine max, differing in genome size and 454 sequencing coverage. Moreover, statistical analysis and visual inspection of the topology of the cluster graphs using a newly developed program tool, SeqGrapheR, were shown to be helpful in distinguishing basic types of repeats and investigating sequence variability within repeat families.Conclusions: Repetitive regions of plant genomes can be efficiently characterized by the presented graph-based analysis and the graph representation of repeats can be further used to assess the variability and evolutionary divergence of repeat families, discover and characterize novel elements, and aid in subsequent assembly of their consensus sequences. © 2010 Novák et al; licensee BioMed Central Ltd.", "date": "2010-07-15T00:00:00Z", "citationCount": 346, "authors": [ { "name": "Novak P." }, { "name": "Neumann P." }, { "name": "Macas J." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btt054", "pmid": "23376349", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "RepeatExplorer: A Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads", "abstract": "Motivation: Repetitive DNA makes up large portions of plant and animal nuclear genomes, yet it remains the least-characterized genome component in most species studied so far. Although the recent availability of high-throughput sequencing data provides necessary resources for in-depth investigation of genomic repeats, its utility is hampered by the lack of specialized bioinformatics tools and appropriate computational resources that would enable large-scale repeat analysis to be run by biologically oriented researchers.Results: Here we present RepeatExplorer, a collection of software tools for characterization of repetitive elements, which is accessible via web interface. A key component of the server is the computational pipeline using a graph-based sequence clustering algorithm to facilitate de novo repeat identification without the need for reference databases of known elements. Because the algorithm uses short sequences randomly sampled from the genome as input, it is ideal for analyzing next-generation sequence reads. Additional tools are provided to aid in classification of identified repeats, investigate phylogenetic relationships of retroelements and perform comparative analysis of repeat composition between multiple species. The server allows to analyze several million sequence reads, which typically results in identification of most high and medium copy repeats in higher plant genomes.Implementation and availability: RepeatExplorer was implemented within the Galaxy environment and set up on a public server at http://repeatexplorer.umbr.cas.cz/. Source code and instructions for local installation are available at http://w3lamc.umbr.cas.cz/ lamc/resources.php.Contact: © 2013 The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. © The Author 2013.", "date": "2013-03-01T00:00:00Z", "citationCount": 523, "authors": [ { "name": "Novak P." }, { "name": "Neumann P." }, { "name": "Pech J." }, { "name": "Steinhaisl J." }, { "name": "MacAs J." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Jiri Macas", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Pavel Neumann", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Petr Novak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Biology Centre, CAS, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Czech Academy of Sciences", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Petr Novak", "email": "petr@umbr.cas.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Petr Novak", "email": "petr@umbr.cas.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2015-11-09T10:32:46Z", "lastUpdate": "2024-11-25T13:58:59.436240Z", "editPermission": { "type": "group", "authors": [ "kavonrtep" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "JPhyloIO", "description": "An open source Java library for reading and writing various tree and alignment formats. Application developers are able to implement format-independent data processing by including event based readers via the abstract strategy pattern. All readers are designed to deal with large amounts of data (alignments with many and/or very long sequences, large trees) without using a great amount of resources (CPU or RAM).", "homepage": "http://bioinfweb.info/JPhyloIO/", "biotoolsID": "jphyloio", "biotoolsCURIE": "biotools:jphyloio", "version": [ "0.5.4" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_3357", "term": "Format detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_3159", "term": "phyloXML" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_3159", "term": "phyloXML" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" } ] }, { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" }, { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_3159", "term": "phyloXML" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" } ] }, { "data": { "uri": "http://edamontology.org/data_1916", "term": "Alignment" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" }, { "uri": "http://edamontology.org/format_1997", "term": "PHYLIP format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_3159", "term": "phyloXML" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" }, { "uri": "http://edamontology.org/format_3160", "term": "NeXML" } ] } ], "note": "Input of type \"XML\" for phylogenetic trees refers to \"XTG\" (http://bioinfweb.info/xmlns/xtg )\nInput of type XML for alignment refers to \"PDE\" the alignment formats of PhyDE (http://phyde.de/ )", "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3070", "term": "Biology" }, { "uri": "http://edamontology.org/topic_3293", "term": "Phylogenetics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "LGPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://twitter.com/bioinfweb", "type": [ "Social media" ], "note": null }, { "url": "https://github.com/bioinfweb/JPhyloIO", "type": [ "Repository" ], "note": null }, { "url": "http://bioinfweb.info/Code/sventon/repos/JPhyloIO/list/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "http://bioinfweb.info/JPhyloIO/Download", "type": "Software package", "note": null, "version": null }, { "url": "http://bioinfweb.info/JPhyloIO/Download", "type": "Software package", "note": null, "version": null }, { "url": "http://bioinfweb.info/JPhyloIO/Download", "type": "API specification", "note": null, "version": null } ], "documentation": [ { "url": "http://bioinfweb.info/JPhyloIO/Documentation", "type": [ "General" ], "note": null }, { "url": "http://bioinfweb.info/JPhyloIO/Documentation/API/Latest/", "type": [ "API documentation" ], "note": null }, { "url": "http://bioinfweb.info/JPhyloIO/Documentation/Demos", "type": [ "Training material" ], "note": null }, { "url": "http://bioinfweb.info/JPhyloIO/License", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bav094", "pmid": "26424081", "pmcid": "PMC4589695", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens", "abstract": "We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of phenoand genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant reusability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work.", "date": "2015-01-01T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Kilian N." }, { "name": "Henning T." }, { "name": "Plitzner P." }, { "name": "Muller A." }, { "name": "Guntsch A." }, { "name": "Stover B.C." }, { "name": "Muller K.F." }, { "name": "Berendsohn W.G." }, { "name": "Borsch T." } ], "journal": "Database" } } ], "credit": [ { "name": "Ben C. Stöver", "email": null, "url": "http://bioinfweb.info/People/Stoever", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sarah Wiechers", "email": "wiechers@bioinfweb.info", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Kai F. Müller", "email": "kaimueller@uni-muenster.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "bioinfweb", "email": null, "url": "http://bioinfweb.info/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Maintainer" ], "note": null }, { "name": "DFG (German Research Foundation)", "email": null, "url": "http://www.dfg.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Ben C. Stöver", "email": null, "url": "http://bioinfweb.info/People/Stoever", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "cbs_admin", "additionDate": "2017-03-30T13:34:34Z", "lastUpdate": "2024-11-25T13:48:04.710657Z", "editPermission": { "type": "group", "authors": [ "BenStoever" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Open PHACTS API", "description": "Open PHACTS Discovery Platform brings together data from multiple publicly available sources of pharmacological and physicochemical information, in order to streamline research and drug discovery processes. The data is integrated into a consolidated triple store, which can be accessed via applications or workflow tools which make use of the Open PHACTS API.", "homepage": "https://dev.openphacts.org/docs/2.1", "biotoolsID": "open_phacts_api", "biotoolsCURIE": "biotools:open_phacts_api", "version": [ "2.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0360", "term": "Structural similarity search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3343", "term": "Compound libraries and screening" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://github.com/openphacts/", "type": [ "Repository" ], "note": null }, { "url": "http://support.openphacts.org/support/home", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://data.openphacts.org/", "type": "Source code", "note": null, "version": null }, { "url": "https://github.com/openphacts/ops-docker", "type": "Container file", "note": "Docker Compose setup", "version": null } ], "documentation": [ { "url": "https://www.openphacts.org/2/sci/data.html", "type": [ "Terms of use" ], "note": null }, { "url": "https://dev.openphacts.org/contact", "type": [ "Citation instructions" ], "note": null }, { "url": "https://dev.openphacts.org/docs/2.0", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.3233/SW-2012-0088", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Applying linked data approaches to pharmacology: Architectural decisions and implementation", "abstract": "The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data. An alpha version of the OPS platform is currently available to the Open PHACTS consortium and a first public release will be made in late 2012, see http://www.openphacts.org/ for details. © 2014 - IOS Press and the authors.", "date": "2014-01-01T00:00:00Z", "citationCount": 49, "authors": [ { "name": "Gray A.J.G." }, { "name": "Groth P." }, { "name": "Loizou A." }, { "name": "Askjaer S." }, { "name": "Brenninkmeijer C." }, { "name": "Burger K." }, { "name": "Chichester C." }, { "name": "Evelo C.T." }, { "name": "Goble C." }, { "name": "Harland L." }, { "name": "Pettifer S." }, { "name": "Thompson M." }, { "name": "Waagmeester A." }, { "name": "Williams A.J." } ], "journal": "Semantic Web" } }, { "doi": "10.1016/j.drudis.2012.05.016", "pmid": "22683805", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Open PHACTS: Semantic interoperability for drug discovery", "abstract": "Open PHACTS is a public-private partnership between academia, publishers, small and medium sized enterprises and pharmaceutical companies. The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies. It is focused on practical and robust applications to solve specific questions in drug discovery research. OPS is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research. This paper lays out the challenges and how the Open PHACTS project is hoping to address these challenges technically and socially. © 2012 Elsevier Ltd.", "date": "2012-11-01T00:00:00Z", "citationCount": 260, "authors": [ { "name": "Williams A.J." }, { "name": "Harland L." }, { "name": "Groth P." }, { "name": "Pettifer S." }, { "name": "Chichester C." }, { "name": "Willighagen E.L." }, { "name": "Evelo C.T." }, { "name": "Blomberg N." }, { "name": "Ecker G." }, { "name": "Goble C." }, { "name": "Mons B." } ], "journal": "Drug Discovery Today" } } ], "credit": [ { "name": "Open PHACTS Foundation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "OpenLink Software", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Innovative Medicines Initiative (IMI)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "cs.manchester.ac.uk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Open PHACTS contact", "email": null, "url": "https://dev.openphacts.org/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Open PHACTS support portal", "email": "support@openphacts.org", "url": "http://support.openphacts.org/support/home", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "soiland-reyes@cs.manchester.ac", "additionDate": "2016-02-18T22:34:41Z", "lastUpdate": "2024-11-25T13:46:36.750725Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Banana Genome Hub", "description": "A Next-Generation Information System for Musa genomics", "homepage": "https://banana-genome-hub.southgreen.fr/", "biotoolsID": "Banana_Genome_Hub", "biotoolsCURIE": "biotools:Banana_Genome_Hub", "version": [ "v2" ], "otherID": [], "relation": [ { "biotoolsID": "southgreen", "type": "includedIn" }, { "biotoolsID": "tripal", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0338", "term": "Sequence database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [], "language": [ "PHP", "JavaScript" ], "license": "GPL-2.0", "collectionID": [ "Genome Hub", "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://banana-genome-hub.southgreen.fr/contact", "type": [ "Helpdesk", "Mailing list" ], "note": null }, { "url": "https://github.com/SouthGreenPlatform/genomehubs", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://banana-genome-hub.southgreen.fr/download", "type": "Biological data", "note": null, "version": null } ], "documentation": [ { "url": "https://banana-genome-hub.southgreen.fr/termofservices", "type": [ "Terms of use" ], "note": null }, { "url": "http://api.tripal.info/api/tripal/2.x", "type": [ "API documentation" ], "note": null }, { "url": "https://banana-genome-hub.southgreen.fr/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bat035", "pmid": "23707967", "pmcid": "PMC3662865", "type": [], "version": null, "note": null, "metadata": { "title": "The banana genome hub", "abstract": "Banana is one of the world's favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. © The Author(s) 2013. Published by Oxford University Press.", "date": "2013-12-01T00:00:00Z", "citationCount": 140, "authors": [ { "name": "Droc G." }, { "name": "Lariviere D." }, { "name": "Guignon V." }, { "name": "Yahiaoui N." }, { "name": "This D." }, { "name": "Garsmeur O." }, { "name": "Dereeper A." }, { "name": "Hamelin C." }, { "name": "Argout X." }, { "name": "Dufayard J.-F." }, { "name": "Lengelle J." }, { "name": "Baurens F.-C." }, { "name": "Cenci A." }, { "name": "Pitollat B." }, { "name": "D'Hont A." }, { "name": "Ruiz M." }, { "name": "Rouard M." }, { "name": "Bocs S." } ], "journal": "Database" } }, { "doi": "10.1038/nature11241", "pmid": "22801500", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The banana (Musa acuminata) genome and the evolution of monocotyledonous plants", "abstract": "Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence. © 2012 Macmillan Publishers Limited. All rights reserved.", "date": "2012-08-09T00:00:00Z", "citationCount": 918, "authors": [ { "name": "D'hont A." }, { "name": "Denoeud F." }, { "name": "Aury J.-M." }, { "name": "Baurens F.-C." }, { "name": "Carreel F." }, { "name": "Garsmeur O." }, { "name": "Noel B." }, { "name": "Bocs S." }, { "name": "Droc G." }, { "name": "Rouard M." }, { "name": "Da Silva C." }, { "name": "Jabbari K." }, { "name": "Cardi C." }, { "name": "Poulain J." }, { "name": "Souquet M." }, { "name": "Labadie K." }, { "name": "Jourda C." }, { "name": "Lengelle J." }, { "name": "Rodier-Goud M." }, { "name": "Alberti A." }, { "name": "Bernard M." }, { "name": "Correa M." }, { "name": "Ayyampalayam S." }, { "name": "Mckain M.R." }, { "name": "Leebens-Mack J." }, { "name": "Burgess D." }, { "name": "Freeling M." }, { "name": "Mbeguie-A-Mbeguie D." }, { "name": "Chabannes M." }, { "name": "Wicker T." }, { "name": "Panaud O." }, { "name": "Barbosa J." }, { "name": "Hribova E." }, { "name": "Heslop-Harrison P." }, { "name": "Habas R." }, { "name": "Rivallan R." }, { "name": "Francois P." }, { "name": "Poiron C." }, { "name": "Kilian A." }, { "name": "Burthia D." }, { "name": "Jenny C." }, { "name": "Bakry F." }, { "name": "Brown S." }, { "name": "Guignon V." }, { "name": "Kema G." }, { "name": "Dita M." }, { "name": "Waalwijk C." }, { "name": "Joseph S." }, { "name": "Dievart A." }, { "name": "Jaillon O." }, { "name": "Leclercq J." }, { "name": "Argout X." }, { "name": "Lyons E." }, { "name": "Almeida A." }, { "name": "Jeridi M." }, { "name": "Dolezel J." }, { "name": "Roux N." }, { "name": "Risterucci A.-M." }, { "name": "Weissenbach J." }, { "name": "Ruiz M." }, { "name": "Glaszmann J.-C." }, { "name": "Quetier F." }, { "name": "Yahiaoui N." }, { "name": "Wincker P." } ], "journal": "Nature" } } ], "credit": [ { "name": "Gaëtan Droc", "email": "gaetan.droc@cirad.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Mathieu Rouard", "email": "m.rouard@cgiar.org", "url": null, "orcidid": "https://orcid.org/0000-0003-1849-1269", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "CIRAD", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Bioversity International", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "ANR", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "owner": "admin", "additionDate": "2019-10-30T13:51:32Z", "lastUpdate": "2024-11-24T20:59:38.690746Z", "editPermission": { "type": "group", "authors": [ "gdroc", "mrouard" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Ocean Gene Atlas", "description": "The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping sequence reads onto gene catalogs).\nUser queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive maps and plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences.", "homepage": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/", "biotoolsID": "Ocean_Gene_Atlas", "biotoolsCURIE": "biotools:Ocean_Gene_Atlas", "version": [], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "mafft", "type": "uses" }, { "biotoolsID": "trimal", "type": "uses" }, { "biotoolsID": "newick_utilities", "type": "uses" }, { "biotoolsID": "hmmer3", "type": "uses" }, { "biotoolsID": "fasttree", "type": "uses" }, { "biotoolsID": "krona", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" }, { "uri": "http://edamontology.org/operation_0573", "term": "Map drawing" }, { "uri": "http://edamontology.org/operation_3478", "term": "Phylogenetic tree reconstruction" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1364", "term": "Hidden Markov model" }, "format": [ { "uri": "http://edamontology.org/format_1370", "term": "HMMER format" } ] }, { "data": { "uri": "http://edamontology.org/data_1138", "term": "Pfam accession number" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2295", "term": "Gene ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_0872", "term": "Phylogenetic tree" }, "format": [ { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] }, { "data": { "uri": 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"http://edamontology.org/topic_3387", "term": "Marine biology" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3941", "term": "Metatranscriptomics" } ], "operatingSystem": [], "language": [ "PHP", "JavaScript" ], "license": "Not licensed", "collectionID": [ "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/build/pdf/Ocean-Gene-Atlas_User_Manual.pdf", "type": [ "User manual", "API documentation" ], "note": null }, { "url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/termsOfUse", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky376", "pmid": "29788376", "pmcid": "PMC6030836", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Ocean Gene Atlas: Exploring the biogeography of plankton genes online", "abstract": "The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.", "date": "2018-07-02T00:00:00Z", "citationCount": 103, "authors": [ { "name": "Villar E." }, { "name": "Vannier T." }, { "name": "Vernette C." }, { "name": "Lescot M." }, { "name": "Cuenca M." }, { "name": "Alexandre A." }, { "name": "Bachelerie P." }, { "name": "Rosnet T." }, { "name": "Pelletier E." }, { "name": "Sunagawa S." }, { "name": "Hingamp P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "oceangeneatlas@mio.osupytheas.fr", "url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "MIO", "email": null, "url": "https://www.mio.osupytheas.fr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "OCEANOMICS", "email": null, "url": "http://www.oceanomics.eu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "ANR-11-BTBR-0008" } ], "owner": "lescot", "additionDate": "2019-11-05T13:33:45Z", "lastUpdate": "2024-11-24T20:59:34.208631Z", "editPermission": { "type": "group", "authors": [ "lescot", "vernette.c" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSAViewer", "description": "Large MSAs visualization interactively on the web.", "homepage": "http://msa.biojs.net", "biotoolsID": "msaviewer", "biotoolsCURIE": "biotools:msaviewer", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1982", "term": "ClustalW format" }, { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1984", "term": "FASTA-aln" } ] }, { "data": { "uri": "http://edamontology.org/data_1711", "term": "Sequence alignment image" }, "format": [ { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_2305", "term": "GFF" } ] } ], "note": "Visualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) 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Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.", "date": "2016-11-15T00:00:00Z", "citationCount": 125, "authors": [ { "name": "Yachdav G." }, { "name": "Wilzbach S." }, { "name": "Rauscher B." }, { "name": "Sheridan R." }, { "name": "Sillitoe I." }, { "name": "Procter J." }, { "name": "Lewis S.E." }, { "name": "Rost B." }, { "name": "Goldberg T." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Sebastian Wilzbach", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ian Sillitoe", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Guy Yachdav", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Benedikt Rauscher", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Tatyana Goldberg", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Technische Universität München", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Google Summer of Code (GSoC) 2014", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BioJS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://github.com/wilzbach/msa", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ana.mravlak", "additionDate": "2016-06-02T02:53:41Z", "lastUpdate": "2024-11-24T20:58:01.008066Z", "editPermission": { "type": "group", "authors": [ "ana.mravlak" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MOLEonline", "description": "Provides a direct access to MOLE functionality and enables on-line and easy-to-use interactive channel analysis.", "homepage": "https://mole.upol.cz/", "biotoolsID": "moleonline", "biotoolsCURIE": "biotools:moleonline", "version": [ "3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0245", "term": "Protein structural motif recognition" }, { "uri": "http://edamontology.org/operation_1816", "term": "Surface rendering" }, { "uri": "http://edamontology.org/operation_0570", "term": "Structure visualisation" }, { "uri": "http://edamontology.org/operation_2241", "term": "Transmembrane protein visualisation" }, { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1539", "term": "Protein structural quality report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1475", "term": "PDB database entry format" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "Identification of channels, tunnels, voids and pores within PDB structure. User-prepared PDB file Either PDB file or structural assemblies Interactive visualisation Annotated PDB file with calculated channels", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_0820", "term": "Membrane and lipoproteins" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "C#" ], "license": "CC-BY-NC-3.0", "collectionID": [ "LCC NCBR", "Czech Republic", "MOLE", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "http://webchem.ncbr.muni.cz/Platform/AppsBin/Mole2_manual.pdf", "type": [ "Repository" ], "note": null }, { "url": "http://webchem.ncbr.muni.cz/Platform/App/Mole", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://webchem.ncbr.muni.cz/Platform/AppsBin/Mole/2.5.17.4.24/Mole2_cmd.zip", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://mole.upol.cz/about", "type": [ "Terms of use" ], "note": null }, { "url": "http://mole.upol.cz/about", "type": [ "Citation instructions" ], "note": null }, { "url": "http://mole.upol.cz/documentation/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks363", "pmid": "22553366", "pmcid": "PMC3394309", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MOLEonline 2.0: Interactive web-based analysis of biomacromolecular channels", "abstract": "Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 108, "authors": [ { "name": "Berka K." }, { "name": "Hanak O." }, { "name": "Sehnal D." }, { "name": "Banas P." }, { "name": "Navratilova V." }, { "name": "Jaiswal D." }, { "name": "Ionescu C.-M." }, { "name": "Svobodova Varekova R." }, { "name": "Koca J." }, { "name": "Otyepka M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gky309", "pmid": "29718451", "pmcid": "PMC6030847", "type": [], "version": null, "note": null, "metadata": { "title": "MOLEonline: A web-based tool for analyzing channels, tunnels and pores (2018 update)", "abstract": "MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLE online for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores.", "date": "2018-07-02T00:00:00Z", "citationCount": 186, "authors": [ { "name": "Pravda L." }, { "name": "Sehnal D." }, { "name": "Tousek D." }, { "name": "Navratilova V." }, { "name": "Bazgier V." }, { "name": "Berka K." }, { "name": "Varekova R.S." }, { "name": "Koca J." }, { "name": "Otyepka M." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "David Sehnal", "email": "david.sehnal@upol.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Michal Otyepka", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ondřej Hanák", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Karel Berka", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Crina-Maria Ionescu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Deepti Jaiswal", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Pavel Banáš", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Jaroslav Koča", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Veronika Navrátilová", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Radka Svobodová Vařeková", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Masaryk University Brno, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Palacký University Olomouc, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": 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Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-12-01T00:00:00Z", "citationCount": 202, "authors": [ { "name": "Smith R.N." }, { "name": "Aleksic J." }, { "name": "Butano D." }, { "name": "Carr A." }, { "name": "Contrino S." }, { "name": "Hu F." }, { "name": "Lyne M." }, { "name": "Lyne R." }, { "name": "Kalderimis A." }, { "name": "Rutherford K." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Wakeling M." }, { "name": "Watkins X." }, { "name": "Micklem G." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gku301", "pmid": "24753429", "pmcid": "PMC4086141", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "InterMine: Extensive web services for modern biology", "abstract": "InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the web interface and can be re-used in many other applications: to find and filter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments, and for other statistical and analysis tools. Here we describe these features and discuss how they can be used separately or in combinations to support integrative and comparative analysis. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 94, "authors": [ { "name": "Kalderimis A." }, { "name": "Lyne R." }, { "name": "Butano D." }, { "name": "Contrino S." }, { "name": "Lyne M." }, { "name": "Heimbach J." }, { "name": "Hu F." }, { "name": "Smith R." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Micklem G." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "University of Cambridge", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "BBSRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Trust", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "NIH", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "gen.cam.ac.uk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "InterMine", "additionDate": "2016-02-04T15:55:00Z", "lastUpdate": "2024-11-24T20:28:49.677323Z", "editPermission": { "type": "group", "authors": [ "rachelyne" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PredictSNP2", "description": "A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.", "homepage": "https://loschmidt.chemi.muni.cz/predictsnp2", "biotoolsID": "predictsnp2", "biotoolsCURIE": "biotools:predictsnp2", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3019", "term": "GVF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "VCF file containing scores and PDF file containing scores and database links", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "Rare Disease", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/", "type": "Downloads page", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1004962", "pmid": "27224906", "pmcid": "PMC4880439", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions", "abstract": "An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.", "date": "2016-05-01T00:00:00Z", "citationCount": 143, "authors": [ { "name": "Bendl J." }, { "name": "Musil M." }, { "name": "Stourac J." }, { "name": "Zendulka J." }, { "name": "Damborsky J." }, { "name": "Brezovsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Jaroslav Bendl", "email": "jaroslav.bendl@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9989-2720", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Milos Musil", "email": "xmusil46@stud.fit.vutbr.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9373-7930", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eric D. Wieben", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jaroslav Zendulka", "email": "zendulka@fit.vut.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-8718-7493", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "International Centre for Clinical Research, Brno, Czech Republic", "email": null, "url": "https://www.fnusa-icrc.org/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Brno University of Technology, Brno, Czech Republic", "email": null, "url": "https://www.vutbr.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "PredictSNP team", "email": "predictsnp@sci.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "European Regional Development Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "European Social Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Grant Agency of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ministry of Education of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Brno University of Technology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Loschmidt Laboratories", "additionDate": "2016-06-30T09:32:44Z", "lastUpdate": "2024-11-24T20:23:08.475881Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CaverDock", "description": "Performs rapid analysis of transport processes in proteins. It models the transportation of a ligand from outside environment into the protein active or binding site and vice versa. It implements a novel algorithm to produce contiguous ligand trajectory and estimation of a binding energy along the pathway. The current version uses CAVER for pathway identification and heavily modified Autodock Vina as a docking engine.", "homepage": "https://loschmidt.chemi.muni.cz/caverdock/", "biotoolsID": "caverdock", "biotoolsCURIE": "biotools:caverdock", "version": [ "1.0", "1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_1957", "term": "raw" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "trajectory of ligand passing through protein tunnel and its energy", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++", "Python" ], "license": "Proprietary", "collectionID": [ "CAVER", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [ { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-14.04.tar.gz", "type": "Binaries", "note": "v1.0, Ubuntu 14.04", "version": "1.0" }, { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-ubuntu-16.04.tar.gz", "type": "Binaries", "note": "v1.0, Ubuntu 16.04", "version": "1.0" }, { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-16.04.tar.xz", "type": "Binaries", "note": "v1.1, Ubuntu 16.04", "version": "1.1" }, { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/caverdock-1.1-ubuntu-18.04.tar.xz", "type": "Binaries", "note": "v1.1, Ubuntu 18.04", "version": "1.1" } ], "documentation": [ { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/manual.pdf", "type": [ "User manual" ], "note": "version 1.0" }, { "url": "https://www.fi.muni.cz/~xfilipov/caverdock/manual-1.1.pdf", "type": [ "User manual" ], "note": "version 1.1" } ], "publication": [ { "doi": "10.1093/bioinformatics/btz386", "pmid": "31077297", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "CaverDock: A molecular docking-based tool to analyse ligand transport through protein tunnels and channels", "abstract": "Motivation: Protein tunnels and channels are key transport pathways that allow ligands to pass between proteins' external and internal environments. These functionally important structural features warrant detailed attention. It is difficult to study the ligand binding and unbinding processes experimentally, while molecular dynamics simulations can be time-consuming and computationally demanding. Results: CaverDock is a new software tool for analysing the ligand passage through the biomolecules. The method uses the optimized docking algorithm of AutoDock Vina for ligand placement docking and implements a parallel heuristic algorithm to search the space of possible trajectories. The duration of the simulations takes from minutes to a few hours. Here we describe the implementation of the method and demonstrate CaverDock's usability by: (i) comparison of the results with other available tools, (ii) determination of the robustness with large ensembles of ligands and (iii) the analysis and comparison of the ligand trajectories in engineered tunnels. Thorough testing confirms that CaverDock is applicable for the fast analysis of ligand binding and unbinding in fundamental enzymology and protein engineering. Availability and implementation: User guide and binaries for Ubuntu are freely available for non-commercial use at https://loschmidt.chemi.muni.cz/caverdock/. The web implementation is available at https://loschmidt.chemi.muni.cz/caverweb/. The source code is available upon request. Supplementary information: Supplementary data are available at Bioinformatics online.", "date": "2019-12-01T00:00:00Z", "citationCount": 55, "authors": [ { "name": "Vavra O." }, { "name": "Filipovic J." }, { "name": "Plhak J." }, { "name": "Bednar D." }, { "name": "Marques S.M." }, { "name": "Brezovsky J." }, { "name": "Stourac J." }, { "name": "Matyska L." }, { "name": "Damborsky J." } ], "journal": "Bioinformatics" } }, { "doi": "10.1109/tcbb.2019.2907492", "pmid": "30932844", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "CaverDock: A Novel Method for the Fast Analysis of Ligand Transport", "abstract": "Here we present a novel method for the analysis of transport processes in proteins and its implementation called CaverDock. Our method is based on a modified molecular docking algorithm. It iteratively places the ligand along the access tunnel in such a way that the ligand movement is contiguous and the energy is minimized. The result of CaverDock calculation is a ligand trajectory and an energy profile of transport process. CaverDock uses the modified docking program Autodock Vina for molecular docking and implements a parallel heuristic algorithm for searching the space of possible trajectories. Our method lies in between the geometrical approaches and molecular dynamics simulations. Contrary to the geometrical methods, it provides an evaluation of chemical forces. However, it is far less computationally demanding and easier to set up compared to molecular dynamics simulations. CaverDock will find a broad use in the fields of computational enzymology, drug design, and protein engineering. The software is available free of charge to the academic users at https://loschmidt.chemi.muni.cz/caverdock/.", "date": "2020-09-01T00:00:00Z", "citationCount": 26, "authors": [ { "name": "Filipovic J." }, { "name": "Vavra O." }, { "name": "Plhak J." }, { "name": "Bednar D." }, { "name": "Marques S.M." }, { "name": "Brezovsky J." }, { "name": "Matyska L." }, { "name": "Damborsk J." } ], "journal": "IEEE/ACM Transactions on Computational Biology and Bioinformatics" } } ], "credit": [ { "name": "Jiri Filipovic", "email": "fila@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-5703-9673", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Ondrej Vavra", "email": "o.vavra@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jan Plhak", "email": "408420@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-6803-0340", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Sergio Marques", "email": "smar96@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6281-7505", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Ludek Matyska", "email": "Ludek.Matyska@muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-6399-5453", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", 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"typeRole": [ "Contributor" ], "note": null }, { "name": "Czech Science Foundation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Brno City Municipality", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Loschmidt Laboratories", "additionDate": "2018-04-06T08:55:47Z", "lastUpdate": "2024-11-24T20:23:05.902530Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CAVER Web", "description": "A web interface for identification and analysis of tunnels and channels in static protein structures with automated starting point detection.", "homepage": "https://loschmidt.chemi.muni.cz/caverweb/", "biotoolsID": 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"type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Caver Web 1.0: Identification of tunnels and channels in proteins and analysis of ligand transport", "abstract": "Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels, and study of the ligands' transport through these transport pathways. Caver Web is the first interactive tool allowing both the analyses within a single graphical user interface. The server is built on top of the abundantly used tunnel detection tool Caver 3.02 and CaverDock 1.0 enabling the study of the ligand transport. The program is easy-to-use as the only required inputs are a protein structure for a tunnel identification and a list of ligands for the transport analysis. The automated guidance procedures assist the users to set up the calculation in a way to obtain biologically relevant results. The identified tunnels, their properties, energy profiles and trajectories for ligands' passages can be calculated and visualized. The tool is very fast (2-20 min per job) and is applicable even for virtual screening purposes. Its simple setup and comprehensive graphical user interface make the tool accessible for a broad scientific community. The server is freely available at https://loschmidt.chemi.muni.cz/caverweb.", "date": "2019-07-01T00:00:00Z", "citationCount": 151, "authors": [ { "name": "Stourac J." }, { "name": "Vavra O." }, { "name": "Kokkonen P." }, { "name": "Filipovic J." }, { "name": "Pinto G." }, { "name": "Brezovsky J." }, { "name": "Damborsky J." }, { "name": "Bednar D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Ondrej Vavra", "email": "o.vavra@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Piia Kokkonen", "email": "piia@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-6002-1856", 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"abstract": "Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. © 2012 Chovancova et al.", "date": "2012-01-01T00:00:00Z", "citationCount": 947, "authors": [ { "name": "Chovancova E." }, { "name": "Pavelka A." }, { "name": "Benes P." }, { "name": "Strnad O." }, { "name": "Brezovsky J." }, { "name": "Kozlikova B." }, { "name": "Gora A." }, { "name": "Sustr V." }, { "name": "Klvana M." }, { "name": "Medek P." }, { "name": "Biedermannova L." }, { "name": "Sochor J." }, { "name": "Damborsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Eva Sebestova", "email": "40707@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], 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Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. © 2012 Chovancova et al.", "date": "2012-01-01T00:00:00Z", "citationCount": 947, "authors": [ { "name": "Chovancova E." }, { "name": "Pavelka A." }, { "name": "Benes P." }, { "name": "Strnad O." }, { "name": "Brezovsky J." }, { "name": "Kozlikova B." }, { "name": "Gora A." }, { "name": "Sustr V." }, { "name": "Klvana M." }, { "name": "Medek P." }, { "name": "Biedermannova L." }, { "name": "Sochor J." }, { "name": "Damborsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Eva Sebestova", "email": "40707@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], 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Two key selection criteria are (i) the predicted solubility and (ii) the sequence identities visualised using an interactive sequence similarity network. The search query can be a sequence from the Swiss-Prot database or a custom sequence with a custom description of essential residues. The output is an interactive selection table containing annotated identified sequences.", "homepage": "https://loschmidt.chemi.muni.cz/enzymeminer/", "biotoolsID": "enzymeminer", "biotoolsCURIE": "biotools:enzymeminer", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" }, { "biotoolsID": "usearch", "type": "uses" }, { "biotoolsID": "clustalo", "type": "uses" }, { "biotoolsID": "tmhmm", "type": "uses" }, { "biotoolsID": "interproscan_4", "type": "uses" }, { "biotoolsID": "soluprot", "type": "uses" }, { "biotoolsID": "bioproject", "type": "uses" }, { "biotoolsID": "ncbi_taxonomy_database", "type": "uses" }, { "biotoolsID": "cytoscape", "type": "uses" }, { "biotoolsID": "mmseqs2", "type": "uses" }, { "biotoolsID": "uniprotkb_swiss-prot", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_0291", "term": "Sequence clustering" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" }, { "uri": "http://edamontology.org/operation_0409", "term": "Protein solubility prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_1233", "term": "Sequence set (protein)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_1245", "term": "Sequence cluster (protein)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/enzymeminer/help", "type": [ "User manual" ], "note": null }, { "url": "https://loschmidt.chemi.muni.cz/enzymeminer/example", "type": [ "Training material" ], "note": null }, { "url": "https://loschmidt.chemi.muni.cz/enzymeminer/terms-of-use", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa372", "pmid": "32392342", "pmcid": "PMC7319543", "type": [], "version": null, "note": null, "metadata": { "title": "EnzymeMiner: Automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities", "abstract": "Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner––a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https://loschmidt.chemi.muni.cz/enzymeminer/.", "date": "2021-01-01T00:00:00Z", "citationCount": 56, "authors": [ { "name": "Hon J." }, { "name": "Borko S." }, { "name": "Stourac J." }, { "name": "Prokop Z." }, { "name": "Zendulka J." }, { "name": "Bednar D." }, { "name": "Martinek T." }, { "name": "Damborsky J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Jiri Hon", "email": "xhonji01@stud.fit.vutbr.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-3321-9629", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Simeon Borko", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Zbynek Prokop", "email": "zbynek@chemi.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9358-4081", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jaroslav Zendulka", "email": "zendulka@fit.vut.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-8718-7493", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-6803-0340", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Tomas Martinek", "email": 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"http://edamontology.org/format_3875", "term": "XTC" }, { "uri": "http://edamontology.org/format_3650", "term": "NetCDF" }, { "uri": "http://edamontology.org/format_3881", "term": "AMBER top" }, { "uri": "http://edamontology.org/format_3910", "term": "trr" }, { "uri": "http://edamontology.org/format_3882", "term": "PSF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "note": "Analysis and visualization of tunnels and channels in proteins", "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "ELIXIR-CZ", "CAVER" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.caver.cz/fil/download/caver_analyst/caver_analyst2_beta2.zip", "type": "Binaries", "note": null, "version": "2.0" }, { "url": "https://caver.cz/index.php?sid=199", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.caver.cz/index.php?sid=123", "type": [ "Citation instructions" ], "note": null }, { "url": "https://caver.cz/fil/download/manual/CAVER_Analyst_2.0_Beta-user_guide.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bty386", "pmid": "29741570", "pmcid": "PMC6184705", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "CAVER Analyst 2.0: Analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories", "abstract": "Motivation Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and proteins with buried binding sites is fundamental to the understanding of their biological function. A detailed analysis of the structural features influencing the transport paths is also important for engineering proteins for biomedical and biotechnological applications. Results CAVER Analyst 2.0 is a software tool for quantitative analysis and real-time visualization of tunnels and channels in static and dynamic structures. This version provides the users with many new functions, including advanced techniques for intuitive visual inspection of the spatiotemporal behavior of tunnels and channels. Novel integrated algorithms allow an efficient analysis and data reduction in large protein structures and molecular dynamic simulations. Availability and implementation CAVER Analyst 2.0 is a multi-platform standalone Java-based application. Binaries and documentation are freely available at www.caver.cz. Supplementary informationSupplementary dataare available at Bioinformatics online.", "date": "2018-10-15T00:00:00Z", "citationCount": 247, "authors": [ { "name": "Jurcik A." }, { "name": "Bednar D." }, { "name": "Byska J." }, { "name": "Marques S.M." }, { "name": "Furmanova K." }, { "name": "Daniel L." }, { "name": "Kokkonen P." }, { "name": "Brezovsky J." }, { "name": "Strnad O." }, { "name": "Stourac J." }, { "name": "Pavelka A." }, { "name": "Manak M." }, { "name": "Damborsky J." }, { "name": "Kozlikova B." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Adam Jurcik", "email": "adikuv@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-6803-0340", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jan Byska", "email": "byska@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Sergio Marques", "email": "smar96@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0002-6281-7505", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Katarina Furmanova", "email": "furmanova@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Lukas Daniel", "email": "211165@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0003-2502-9224", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Piia Kokkonen", "email": "piia@mail.muni.cz", "url": null, 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"additionDate": "2015-11-07T20:36:20Z", "lastUpdate": "2024-11-24T20:22:56.347730Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PredictSNP", "description": "A consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.", "homepage": "https://loschmidt.chemi.muni.cz/predictsnp1", "biotoolsID": "predictsnp", "biotoolsCURIE": "biotools:predictsnp", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "mapp", "type": "uses" }, { "biotoolsID": "nssnpanalyzer", "type": "uses" }, { "biotoolsID": "panther", "type": "uses" }, { "biotoolsID": "phd-snp", "type": "uses" }, { "biotoolsID": "polyphen", "type": "uses" }, { "biotoolsID": "polyphen-2", "type": "uses" }, { "biotoolsID": "sift", "type": "uses" }, { "biotoolsID": "snap", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] } ], "note": "Prediction of the effect of amino acid substitution on protein function", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java", "Python" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "Rare Disease", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp1/docs/predictsnp-1.0.tar.gz", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp1/docs/USER_GUIDE.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1003440", "pmid": "24453961", "pmcid": "PMC3894168", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations", "abstract": "Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. © 2014 Bendl et al.", "date": "2014-01-01T00:00:00Z", "citationCount": 595, "authors": [ { "name": "Bendl J." }, { "name": "Stourac J." }, { "name": "Salanda O." }, { "name": "Pavelka A." }, { "name": "Wieben E.D." }, { "name": "Zendulka J." }, { "name": "Brezovsky J." }, { "name": "Damborsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Jaroslav Bendl", "email": "jaroslav.bendl@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9989-2720", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Ondrej Salanda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eric D. Wieben", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jaroslav Zendulka", "email": "zendulka@fit.vut.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-8718-7493", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "International Centre for Clinical Research, Brno, Czech Republic", "email": null, "url": "https://www.fnusa-icrc.org/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Brno University of Technology, Brno, Czech Republic", "email": null, "url": "https://www.vutbr.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Mayo Clinic, Rochester, New York, United States of America", "email": null, "url": "https://www.mayoclinic.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "PredictSNP team", "email": "predictsnp@sci.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "European Regional Development Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "European Social Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Grant Agency of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ministry of Education of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Brno University of Technology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Loschmidt Laboratories", "additionDate": "2015-11-07T20:40:08Z", "lastUpdate": "2024-11-24T20:22:54.522074Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SETTER", "description": "A web application for RNA structure comparison.", "homepage": "http://setter.projekty.ms.mff.cuni.cz/", "biotoolsID": "setter", "biotoolsCURIE": "biotools:setter", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2481", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/operation_0502", "term": "RNA secondary structure alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0881", "term": "Secondary structure alignment (RNA)" }, "format": [] } ], "note": "Secondary-based RNA tertiary structure superposition either PDBID or user-prepared PDB", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0099", "term": "RNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" } ], "operatingSystem": [ "Linux" ], "language": [ "C++", "Python" ], "license": null, "collectionID": [ "Czech Republic", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://setter.projekty.ms.mff.cuni.cz/help/index/", "type": [ "Citation instructions", "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gks560", "pmid": "22693209", "pmcid": "PMC3394248", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SETTER: Web server for RNA structure comparison", "abstract": "The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n 2) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 22, "authors": [ { "name": "Cech P." }, { "name": "Svozil D." }, { "name": "Hoksza D." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1186/s12859-015-0696-8", "pmid": "26264783", "pmcid": "PMC4531852", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "MultiSETTER: Web server for multiple RNA structure comparison", "abstract": "Background: Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results: In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion: To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.", "date": "2015-08-12T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Cech P." }, { "name": "Hoksza D." }, { "name": "Svozil D." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1109/tcbb.2014.2351810", "pmid": "26357263", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Multiple 3D RNA structure superposition using neighbor joining", "abstract": "Recent advances in RNA research and the steady growth of available RNA structures call for bioinformatics methods for handling and analyzing RNA structural data. Recently, we introduced SETTER - a fast and accurate method for RNA pairwise structure alignment. In this paper, we describe MultiSETTER, SETTER extension for multiple RNA structure alignment. MultiSETTER combines SETTER's decomposition of RNA structures into non-overlapping structural subunits with the multiple sequence alignment algorithm ClustalW adapted for the structure alignment. The accuracy of MultiSETTER was assessed by the automatic classification of RNA structures and its comparison to SCOR annotations. In addition, MultiSETTER classification was also compared to multiple sequence alignment-based and secondary structure alignment-based classifications provided by LocARNA and RNADistance tools, respectively. MultiSETTER precompiled Windows libraries, as well as the C++ source code, are freely available from http://siret.cz/multisetter.", "date": "2015-05-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Hoksza D." }, { "name": "Svozil D." } ], "journal": "IEEE/ACM Transactions on Computational Biology and Bioinformatics" } } ], "credit": [ { "name": "Petr Čech", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "David Hoksza", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Daniel Svozil", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Daniel Svozil", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "Charles University in Prague, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "University of Chemistry and Technology Prague, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Czech Science Foundation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Daniel Svozil", "email": "svozild@vscht.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "David Hoksza", "email": "david.hoksza@mff.cuni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "Daniel Svozil", "email": "svozild@vscht.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Hoksza", "email": "david.hoksza@mff.cuni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2015-11-25T19:04:17Z", "lastUpdate": "2024-11-24T20:22:35.598559Z", "editPermission": { "type": "group", "authors": [ "davidhokszamff", "mar_nov" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Clustal Omega", "description": "Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.", "homepage": "http://www.clustal.org/omega/", "biotoolsID": "clustalo", "biotoolsCURIE": "biotools:clustalo", "version": [ "1.0 - 1.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [ "clustal", "Bioconda", "galaxyPasteur", "DebianMed" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/?tool_id=toolshed.pasteur.fr%2Frepos%2Fdcorreia%2Fclustalo%2Fclustalo%2F1.2.1.1&version=1.2.1.1&__identifer=9si4ugr4fwu", "type": [ "Galaxy service" ], "note": null }, { "url": "http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.clustal.org/omega/#Download", "type": "Downloads page", "note": null, "version": null }, { "url": "https://tracker.debian.org/pkg/clustalo", "type": "Software package", "note": "Debian package (Debian Med Packaging Team). Source code package 'clustalo' and binary packages including API and its documentation.", "version": null }, { "url": "https://bioconda.github.io/recipes/clustalo/README.html", "type": "Software package", "note": "Conda package (Bioconda channel). Conda recipe at https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clustalo/meta.yaml", "version": null } ], "documentation": [ { "url": "http://www.clustal.org/omega/#Documentation", "type": [ "General" ], "note": null }, { "url": "http://www.clustal.org/omega/README", "type": [ "User manual" ], "note": "Clustal README file" }, { "url": "http://www.clustal.org/omega/INSTALL", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1038/msb.2011.75", "pmid": "21988835", "pmcid": "PMC3261699", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega", "abstract": "Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam. © 2011 EMBO and Macmillan Publishers Limited All rights reserved.", "date": "2011-10-19T00:00:00Z", "citationCount": 11023, "authors": [ { "name": "Sievers F." }, { "name": "Wilm A." }, { "name": "Dineen D." }, { "name": "Gibson T.J." }, { "name": "Karplus K." }, { "name": "Li W." }, { "name": "Lopez R." }, { "name": "McWilliam H." }, { "name": "Remmert M." }, { "name": "Soding J." }, { "name": "Thompson J.D." }, { "name": "Higgins D.G." } ], "journal": "Molecular Systems Biology" } }, { "doi": "10.1002/pro.3290", "pmid": "28884485", "pmcid": "PMC5734385", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Clustal Omega for making accurate alignments of many protein sequences", "abstract": "Clustal Omega is a widely used package for carrying out multiple sequence alignment. Here, we describe some recent additions to the package and benchmark some alternative ways of making alignments. These benchmarks are based on protein structure comparisons or predictions and include a recently described method based on secondary structure prediction. In general, Clustal Omega is fast enough to make very large alignments and the accuracy of protein alignments is high when compared to alternative packages. The package is freely available as executables or source code from www.clustal.org or can be run on-line from a variety of sites, especially the EBI www.ebi.ac.uk.", "date": "2018-01-01T00:00:00Z", "citationCount": 1148, "authors": [ { "name": "Sievers F." }, { "name": "Higgins D.G." } ], "journal": "Protein Science" } }, { "doi": "10.1002/0471250953.bi0313s48", "pmid": "25501942", "pmcid": null, "type": [ "Usage" ], "version": null, "note": "How to use Clustal Omega. Not open access.", "metadata": { "title": "Clustal Omega", "abstract": "Clustal Omega is a package for making multiple sequence alignments of amino acid or nucleotide sequences, quickly and accurately. It is a complete upgrade and rewrite of earlier Clustal programs. This unit describes how to run Clustal Omega interactively from a command line, although it can also be run online from several sites. The unit describes a basic protocol for taking a set of unaligned sequences and producing a full alignment. There are also protocols for using an external HMM or iteration to help improve an alignment.", "date": "2014-01-01T00:00:00Z", "citationCount": 414, "authors": [ { "name": "Sievers F." }, { "name": "Higgins D.G." } ], "journal": "Current Protocols in Bioinformatics" } } ], "credit": [ { "name": "Clustal helpdesk", "email": "clustalw@ucd.ie", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Science Foundation Ireland", "email": null, "url": "http://www.sfi.ie/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "owner": "hmenager", "additionDate": "2016-12-19T14:28:44Z", "lastUpdate": "2024-11-24T20:19:47.776845Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CyGenexpi", "description": "CyGenexpi is a Cytoscape plugin for validating/inferring genetic networks from time series expression data. It is based on a ordinary differential equation (ODE) model of gene regulation.", "homepage": "https://github.com/cas-bioinf/genexpi/wiki/CyGenexpi", "biotoolsID": "CyGenexpi", "biotoolsCURIE": "biotools:CyGenexpi", "version": [ "1.4.2", "1.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1781", "term": "Gene regulatory network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2984", "term": "Pathway or network report" }, "format": [ { "uri": "http://edamontology.org/format_3751", "term": "DSV" } ] } ], "note": "More info at https://github.com/cas-bioinf/genexpi/wiki/Example", "cmd": "Use the menu item Apps -> Genexpi -> Genexpi Wizard" } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0204", "term": "Gene regulation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "LGPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/cas-bioinf/genexpi", "type": [ "Repository" ], "note": null }, { "url": "http://apps.cytoscape.org/apps/cygenexpi", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://apps.cytoscape.org/apps/cygenexpi", "type": "Downloads page", "note": null, "version": "1.4.2" }, { "url": "https://github.com/cas-bioinf/genexpi", "type": "Source code", "note": null, "version": "1.4.2" } ], "documentation": [ { "url": "https://github.com/cas-bioinf/genexpi/wiki/CyGenexpi", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-018-2138-x", "pmid": "29653518", "pmcid": "PMC5899412", "type": [], "version": "1.3.0", "note": null, "metadata": { "title": "Genexpi: A toolset for identifying regulons and validating gene regulatory networks using time-course expression data", "abstract": "Background: Identifying regulons of sigma factors is a vital subtask of gene network inference. Integrating multiple sources of data is essential for correct identification of regulons and complete gene regulatory networks. Time series of expression data measured with microarrays or RNA-seq combined with static binding experiments (e.g., ChIP-seq) or literature mining may be used for inference of sigma factor regulatory networks. Results: We introduce Genexpi: a tool to identify sigma factors by combining candidates obtained from ChIP experiments or literature mining with time-course gene expression data. While Genexpi can be used to infer other types of regulatory interactions, it was designed and validated on real biological data from bacterial regulons. In this paper, we put primary focus on CyGenexpi: a plugin integrating Genexpi with the Cytoscape software for ease of use. As a part of this effort, a plugin for handling time series data in Cytoscape called CyDataseries has been developed and made available. Genexpi is also available as a standalone command line tool and an R package. Conclusions: Genexpi is a useful part of gene network inference toolbox. It provides meaningful information about the composition of regulons and delivers biologically interpretable results.", "date": "2018-04-13T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Modrak M." }, { "name": "Vohradsky J." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Martin Modrák", "email": "martin.modrak@biomed.cas.cz", "url": null, "orcidid": "http://orcid.org/0000-0002-8886-7797", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Ministry of Education, Youth and Sports of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "C4Sys research infrastructure project (MEYS project No: LM20150055), and ELIXIR_CZ project (MEYS project no. LM2015047)" } ], "owner": "modrak_m", "additionDate": "2019-07-02T12:41:10Z", "lastUpdate": "2024-11-24T20:17:46.610252Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cancer Genome Interpreter (CGI)", "description": "Cancer Genome Interpreter (CGI) is designed to support the identification of tumor alterations that drive the disease and detect those that may be therapeutically actionable. CGI relies on existing knowledge collected from several resources and on computational methods that annotate the alterations in a tumor according to distinct levels of evidence.", "homepage": "https://www.cancergenomeinterpreter.org/", "biotoolsID": "cgi", "biotoolsCURIE": "biotools:cgi", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "boostdm", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_3275", "term": "Phenotype name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1270", "term": "Feature table" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Identifying all the potential driver genes on a list of somatic mutations.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3275", "term": "Phenotype name" }, "format": [ { "uri": "http://edamontology.org/format_1964", "term": "plain text format (unformatted)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": "Providing list of biomarkers and cancer treatments based on genomic annotations", "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python", "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "BBG genomic tools", "RIS3CAT VEIS" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.cancergenomeinterpreter.org", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.cancergenomeinterpreter.org/faq", "type": [ "FAQ", "User manual", "General" ], "note": null }, { "url": "https://creativecommons.org/licenses/by-nc/4.0/", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1186/s13073-018-0531-8", "pmid": "29592813", "pmcid": "PMC5875005", "type": [], "version": null, "note": null, "metadata": { "title": "Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations", "abstract": "While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Interpreter, a versatile platform that automates the interpretation of newly sequenced cancer genomes, annotating the potential of alterations detected in tumors to act as drivers and their possible effect on treatment response. The results are organized in different levels of evidence according to current knowledge, which we envision can support a broad range of oncology use cases. The resource is publicly available at http://www.cancergenomeinterpreter.org.", "date": "2018-03-28T00:00:00Z", "citationCount": 354, "authors": [ { "name": "Tamborero D." }, { "name": "Rubio-Perez C." }, { "name": "Deu-Pons J." }, { "name": "Schroeder M.P." }, { "name": "Vivancos A." }, { "name": "Rovira A." }, { "name": "Tusquets I." }, { "name": "Albanell J." }, { "name": "Rodon J." }, { "name": "Tabernero J." }, { "name": "de Torres C." }, { "name": "Dienstmann R." }, { "name": "Gonzalez-Perez A." }, { "name": "Lopez-Bigas N." } ], "journal": "Genome Medicine" } } ], "credit": [ { "name": "La Marato TV3", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European Research Council", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "AECC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Spanish Ministry of Economy and Competitiveness", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "H2020-EU.3.1.6. - Health care provision and integrated care", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "AGAUR", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "UPF", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "IRB Barcelona", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "nlopezb", "additionDate": "2020-12-21T12:36:03Z", "lastUpdate": "2024-11-24T20:16:52.724131Z", "editPermission": { "type": "group", "authors": [ "Iker", "jordi.deu@upf.edu", "sgonzal" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PDB-REDO databank of optimised macromolecular structures", "description": "Databank of optimised macromolecular structures. PDB-REDO entries are refined, rebuilt and validated with one consistent protocol using the equivalent entry in the Protein Data Bank and its experimental data. PDB-REDO entries typically have higher structural quality and a better fit to the experimental data.", "homepage": "https://pdb-redo.eu", "biotoolsID": "pdb-redo", "biotoolsCURIE": "biotools:pdb-redo", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1477", "term": "mmCIF" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "data": { "uri": "http://edamontology.org/data_1539", "term": "Protein structural quality report" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0937", "term": "Electron density map" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [ { "uri": "http://edamontology.org/format_1454", "term": "dssp" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Freeware", "collectionID": [ "3D-BioInfo", "DRCAT", "3D-BioInfo-Structure-Function", "3D-BioInfo-Nucleic-Acid", "3D-BioInfo-Protein-Ligand-Interactions", "INSTRUCT" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [ { "url": "https://pdb-redo.eu/download-info.html", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://pdb-redo.eu", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1107/s0907444911054515", "pmid": "22505269", "pmcid": "PMC3322608", "type": [], "version": null, "note": null, "metadata": { "title": "PDB-REDO: Constructive validation, more than just looking for errors", "abstract": "Developments of the PDB-REDO procedure that combine re-refinement and rebuilding within a unique decision-making framework to improve structures in the PDB are presented. PDB-REDO uses a variety of existing and custom-built software modules to choose an optimal refinement protocol (e.g. anisotropic, isotropic or overall B-factor refinement, TLS model) and to optimize the geometry versus data-refinement weights. Next, it proceeds to rebuild side chains and peptide planes before a final optimization round. PDB-REDO works fully automatically without the need for intervention by a crystallographic expert. The pipeline was tested on 12 000 PDB entries and the great majority of the test cases improved both in terms of crystallographic criteria such as R free and in terms of widely accepted geometric validation criteria. It is concluded that PDB-REDO is useful to update the otherwise static structures in the PDB to modern crystallographic standards. The publically available PDB-REDO database provides better model statistics and contributes to better refinement and validation targets. © International Union of Crystallography 2012.", "date": "2012-04-01T00:00:00Z", "citationCount": 179, "authors": [ { "name": "Joosten R.P." }, { "name": "Joosten K." }, { "name": "Murshudov G.N." }, { "name": "Perrakis A." } ], "journal": "Acta Crystallographica Section D: Biological Crystallography" } }, { "doi": "10.1107/s0021889809008784", "pmid": "22477769", "pmcid": "PMC3246819", "type": [], "version": null, "note": null, "metadata": { "title": "PDB-REDO: Automated re-refinement of X-ray structure models in the PDB", "abstract": "Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB-REDO databank (http://www.cmbi.ru.nl/pdb-redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour. © 2009 International Union of Crystallography.", "date": "2009-01-01T00:00:00Z", "citationCount": 185, "authors": [ { "name": "Joosten R.P." }, { "name": "Salzemann J." }, { "name": "Bloch V." }, { "name": "Stockinger H." }, { "name": "Berglund A.-C." }, { "name": "Blanchet C." }, { "name": "Bongcam-Rudloff E." }, { "name": "Combet C." }, { "name": "Da Costa A.L." }, { "name": "Deleage G." }, { "name": "Diarena M." }, { "name": "Fabbretti R." }, { "name": "Fettahi G." }, { "name": "Flegel V." }, { "name": "Gisel A." }, { "name": "Kasam V." }, { "name": "Kervinen T." }, { "name": "Korpelainen E." }, { "name": "Mattila K." }, { "name": "Pagni M." }, { "name": "Reichstadt M." }, { "name": "Breton V." }, { "name": "Tickle I.J." }, { "name": "Vriend G." } ], "journal": "Journal of Applied Crystallography" } }, { "doi": "10.1107/s0907444908037591", "pmid": "19171973", "pmcid": "PMC2631631", "type": [], "version": null, "note": null, "metadata": { "title": "Re-refinement from deposited X-ray data can deliver improved models for most PDB entries", "abstract": "The deposition of X-ray data along with the customary structural models defining PDB entries makes it possible to apply large-scale re-refinement protocols to these entries, thus giving users the benefit of improvements in X-ray methods that have occurred since the structure was deposited. Automated gradient refinement is an effective method to achieve this goal, but real-space intervention is most often required in order to adequately address problems detected by structure-validation software. In order to improve the existing protocol, automated re-refinement was combined with structure validation and difference-density peak analysis to produce a catalogue of problems in PDB entries that are amenable to automatic correction. It is shown that re-refinement can be effective in producing improvements, which are often associated with the systematic use of the TLS parameterization of B factors, even for relatively new and high-resolution PDB entries, while the accompanying manual or semi-manual map analysis and fitting steps show good prospects for eventual automation. It is proposed that the potential for simultaneous improvements in methods and in re-refinement results be further encouraged by broadening the scope of depositions to include refinement metadata and ultimately primary rather than reduced X-ray data.", "date": "2009-01-20T00:00:00Z", "citationCount": 69, "authors": [ { "name": "Joosten R.P." }, { "name": "Womack T." }, { "name": "Vriend G." }, { "name": "Bricogne G." } ], "journal": "Acta Crystallographica Section D: Biological Crystallography" } }, { "doi": "10.1107/s2052252518010552", "pmid": "30224962", "pmcid": "PMC6126648", "type": [], "version": null, "note": null, "metadata": { "title": "Homology-based loop modeling yields more complete crystallographic protein structures", "abstract": "Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.", "date": "2018-01-01T00:00:00Z", "citationCount": 22, "authors": [ { "name": "Van Beusekom B." }, { "name": "Joosten K." }, { "name": "Hekkelman M.L." }, { "name": "Joosten R.P." }, { "name": "Perrakis A." } ], "journal": "IUCrJ" } }, { "doi": "10.1002/pro.3353", "pmid": "29168245", "pmcid": "PMC5818736", "type": [ "Method" ], "version": "7", "note": "Algorithms for homology restrains; new databank", "metadata": { "title": "Homology-based hydrogen bond information improves crystallographic structures in the PDB", "abstract": "The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset.", "date": "2018-03-01T00:00:00Z", "citationCount": 41, "authors": [ { "name": "van Beusekom B." }, { "name": "Touw W.G." }, { "name": "Tatineni M." }, { "name": "Somani S." }, { "name": "Rajagopal G." }, { "name": "Luo J." }, { "name": "Gilliland G.L." }, { "name": "Perrakis A." }, { "name": "Joosten R.P." } ], "journal": "Protein Science" } }, { "doi": "10.1093/bioinformatics/btr590", "pmid": "22034521", "pmcid": "PMC3232375", "type": [ "Method" ], "version": null, "note": "Algorithms for model rebuilding", "metadata": { "title": "Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank", "abstract": "Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. Results: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. © The Author(s) 2011. Published by Oxford University Press.", "date": "2011-12-01T00:00:00Z", "citationCount": 85, "authors": [ { "name": "Joosten R.P." }, { "name": "Joosten K." }, { "name": "Cohen S.X." }, { "name": "Vriend G." }, { "name": "Perrakis A." } ], "journal": "Bioinformatics" } }, { "doi": "10.1016/j.jmb.2016.02.002", "pmid": "26869101", "pmcid": null, "type": [ "Method" ], "version": null, "note": "Algorithms for correction and completion of N-glycosylation sites", "metadata": { "title": "New Biological Insights from Better Structure Models", "abstract": "Structure validation is a key component of all steps in the structure determination process, from structure building, refinement, deposition, and evaluation all the way to post-deposition optimisation of structures in the Protein Data Bank (PDB) by re-refinement and re-building. Today, many aspects of protein structures are understood better than 10 years ago, and combined with improved software and more computing power, the automated PDB-REDO procedure can significantly improve about 85% of all X-ray structures ever deposited in the PDB. We review structure validation, structure improvement, and a series of validation resources and facilities that give access to improved PDB files and to reports on the quality of the original and the improved structures. Post-deposition optimisation generally leads to improved protein structures and a series of examples will illustrate how that, in turn, leads to improved or even novel biological insights.", "date": "2016-03-27T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Touw W.G." }, { "name": "Joosten R.P." }, { "name": "Vriend G." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1107/s2059798316013036", "pmid": "27710932", "pmcid": "PMC5053137", "type": [], "version": null, "note": null, "metadata": { "title": "Validation and correction of ZnCysxHisy complexes", "abstract": "Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average ZnCys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more contextsensitive targets for model validation and refinement.", "date": "2016-01-01T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Touw W.G." }, { "name": "Van Beusekom B." }, { "name": "Evers J.M.G." }, { "name": "Vriend G." }, { "name": "Joosten R.P." } ], "journal": "Acta Crystallographica Section D: Structural Biology" } }, { "doi": "10.1107/s2059798319003875", "pmid": "30988258", "pmcid": "PMC6465985", "type": [], "version": null, "note": null, "metadata": { "title": "Building and rebuilding N-glycans in protein structure models", "abstract": "N-Glycosylation is one of the most common post-translational modifications and is implicated in, for example, protein folding and interaction with ligands and receptors. N-Glycosylation trees are complex structures of linked carbohydrate residues attached to asparagine residues. While carbohydrates are typically modeled in protein structures, they are often incomplete or have the wrong chemistry. Here, new tools are presented to automatically rebuild existing glycosylation trees, to extend them where possible, and to add new glycosylation trees if they are missing from the model. The method has been incorporated in the PDB-REDO pipeline and has been applied to build or rebuild 16 452 carbohydrate residues in 11 651 glycosylation trees in 4498 structure models, and is also available from the PDB-REDO web server. With better modeling of N-glycosylation, the biological function of this important modification can be better and more easily understood.", "date": "2019-04-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "van Beusekom B." }, { "name": "Wezel N." }, { "name": "Hekkelman M.L." }, { "name": "Perrakis A." }, { "name": "Emsley P." }, { "name": "Joosten R.P." } ], "journal": "Acta Crystallographica Section D: Structural Biology" } } ], "credit": [ { "name": "Robbie P. Joosten", "email": "r.joosten@nki.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-2323-2686", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Gert Vriend", "email": "vriend@cmbi.ru.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": "Project initiator" }, { "name": "Anastassis Perrakis", "email": "a.perrakis@nki.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-1151-6227", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Maarten Hekkelman", "email": "m.hekkelman@nki.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Bart van Beusekom", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Krista Joosten", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Netherlands Organization for Scientific Research (NWO)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": "Various grants (Veni, Vidi, TOP)" }, { "name": "West-Life Horizon 2020", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "iNEXT", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "Wouter Touw", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "The Netherlands Cancer Institute", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "CCP4", "email": null, "url": "https://www.ccp4.ac.uk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Contributor" ], "note": "Financial and other support" } ], "owner": "rjoosten", "additionDate": "2015-10-07T18:29:49Z", "lastUpdate": "2024-11-24T20:12:11.088870Z", "editPermission": { "type": "group", "authors": [ "rjoosten" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CalFitter", "description": "Unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. Allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways.", "homepage": "https://loschmidt.chemi.muni.cz/calfitter/", "biotoolsID": "calfitter", "biotoolsCURIE": "biotools:calfitter", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2415", "term": "Protein folding analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental measurement" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_3569", "term": "Applied mathematics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java", "Python" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/calfitter/?action=help&", "type": [ "User manual" ], "note": null }, { "url": "https://loschmidt.chemi.muni.cz/calfitter/?action=example&", "type": [ "Training material" ], "note": null }, { "url": "https://loschmidt.chemi.muni.cz/calfitter/?action=terms&", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky358", "pmid": "29762722", "pmcid": "PMC6031030", "type": [], "version": "1.3", "note": null, "metadata": { "title": "CalFitter: A web server for analysis of protein thermal denaturation data", "abstract": "Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.", "date": "2018-07-02T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Mazurenko S." }, { "name": "Stourac J." }, { "name": "Kunka A." }, { "name": "Nedeljkovic S." }, { "name": "Bednar D." }, { "name": "Prokop Z." }, { "name": "Damborsky J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac378", "pmid": "35580052", "pmcid": "PMC9252748", "type": [], "version": "2.0", "note": null, "metadata": { "title": "CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability", "abstract": "The importance of the quantitative description of protein unfolding and aggregation for the rational design of stability or understanding the molecular basis of protein misfolding diseases is well established. Protein thermostability is typically assessed by calorimetric or spectroscopic techniques that monitor different complementary signals during unfolding. The CalFitter webserver has already proved integral to deriving invaluable energy parameters by global data analysis. Here, we introduce CalFitter 2.0, which newly incorporates singular value decomposition (SVD) of multi-wavelength spectral datasets into the global fitting pipeline. Processed time- or temperature-evolved SVD components can now be fitted together with other experimental data types. Moreover, deconvoluted basis spectra provide spectral fingerprints of relevant macrostates populated during unfolding, which greatly enriches the information gains of the CalFitter output. The SVD analysis is fully automated in a highly interactive module, providing access to the results to users without any prior knowledge of the underlying mathematics. Additionally, a novel data uploading wizard has been implemented to facilitate rapid and easy uploading of multiple datasets. Together, the newly introduced changes significantly improve the user experience, making this software a unique, robust, and interactive platform for the analysis of protein thermal denaturation data. The webserver is freely accessible at https://loschmidt.chemi.muni.cz/calfitter.", "date": "2022-07-05T00:00:00Z", "citationCount": 4, "authors": [ { "name": "Kunka A." }, { "name": "Lacko D." }, { "name": "Stourac J." }, { "name": "Damborsky J." }, { "name": "Prokop Z." }, { "name": "Mazurenko S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Stanislav Mazurenko", "email": "stan.mazurenko@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3659-4819", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Antonin Kunka", "email": "393392@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Sava Nedeljkovic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "David Bednar", "email": "222755@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-6803-0340", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Zbynek Prokop", "email": "zbynek@chemi.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9358-4081", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "International Centre for Clinical Research, Brno, Czech Republic", "email": null, "url": "https://www.fnusa-icrc.org/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Brno University of Technology, Brno, Czech Republic", "email": null, "url": "https://www.vutbr.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "CalFitter team", "email": "calfitter@sci.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Czech Science Foundation", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ministry of Education of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "European Union", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Brno City Municipality", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Loschmidt Laboratories", "additionDate": "2018-07-04T13:50:50Z", "lastUpdate": "2024-11-24T15:37:32.557978Z", "editPermission": { "type": "group", "authors": [ "zuramiko" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HADDOCK", "description": "High Ambiguity Driven biomolecular DOCKing: an information-driven flexible docking approach for the modeling of biomolecular complexes. It distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. It can deal with a large class of modeling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.", "homepage": "http://www.bonvinlab.org/software/haddock2.4/", "biotoolsID": "haddock", "biotoolsCURIE": "biotools:haddock", "version": [ "2.2", "2.4" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service", "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": null, "collectionID": [ "BioExcel", "WeNMR", "WestLife", "EOSC-Hub", "INSTRUCT" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "http://www.bonvinlab.org/software/haddock2.2", "type": [ "Repository" ], "note": "HADDOCK2.2 software page" }, { "url": "http://www.bonvinlab.org/software/haddock2.4", "type": [ "Repository" ], "note": "HADDOCK2.4 software page" }, { "url": "https://wenmr.science.uu.nl/haddock2.4", "type": [ "Service" ], "note": "HADDOCK2.4 web server" }, { "url": "https://ask.bioexcel.eu/c/haddock", "type": [ "Discussion forum" ], "note": "HADDOCK forum" } ], "download": [ { "url": "http://www.bonvinlab.org/software/haddock2.4/download/", "type": "Downloads page", "note": null, "version": "2.4" } ], "documentation": [ { "url": "http://www.bonvinlab.org/education/", "type": [ "Training material" ], "note": "Various tutorials describing the use of the HADDOCK server for various scenarios.; Tutorial" }, { "url": "https://youtu.be/KUbEwGv21n8", "type": [ "Training material" ], "note": "Recording of a lecture of Prof. Bonvin at the CECAM BImMS 2019 workshop in Lugano (Oct. 7th, 2019)" }, { "url": "http://www.bonvinlab.org/software/haddock2.2/manual/", "type": [ "User manual" ], "note": "HADDOCK2.2 online manual" }, { "url": "http://www.bonvinlab.org/software/haddock2.4/manual/", "type": [ "User manual" ], "note": "HADDOCK2.4 online manual" }, { "url": "https://www.youtube.com/watch?v=AULTBI3BqRY", "type": [ "Training material" ], "note": "BioExcel2020 summerschool - Integrative modelling lecture by Alexandre Bonvin" } ], "publication": [ { "doi": "10.1016/j.jmb.2015.09.014", "pmid": "26410586", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes", "abstract": "The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.", "date": "2016-02-22T00:00:00Z", "citationCount": 1929, "authors": [ { "name": "Van Zundert G.C.P." }, { "name": "Rodrigues J.P.G.L.M." }, { "name": "Trellet M." }, { "name": "Schmitz C." }, { "name": "Kastritis P.L." }, { "name": "Karaca E." }, { "name": "Melquiond A.S.J." }, { "name": "Van Dijk M." }, { "name": "De Vries S.J." }, { "name": "Bonvin A.M.J.J." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1021/ja026939x", "pmid": "12580598", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HADDOCK: A protein-protein docking approach based on biochemical or biophysical information", "abstract": "The structure determination of protein-protein complexes is a rather tedious and lengthy process, by both NMR and X-ray crystallography. Several methods based on docking to study protein complexes have also been well developed over the past few years. Most of these approaches are not driven by experimental data but are based on a combination of energetics and shape complementarity. Here, we present an approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process. An AIR is defined as an ambiguous distance between all residues shown to be involved in the interaction. The accuracy of our approach is demonstrated with three molecular complexes. For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titration data were available. Mutagenesis data were used in the last example. In all cases, the best structures generated by HADDOCK, that is, the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0 Å backbone RMSD).", "date": "2003-02-15T00:00:00Z", "citationCount": 2472, "authors": [ { "name": "Dominguez C." }, { "name": "Boelens R." }, { "name": "Bonvin A.M.J.J." } ], "journal": "Journal of the American Chemical Society" } }, { "doi": "10.1016/j.str.2015.03.014", "pmid": "25914056", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-electron microscopy data", "abstract": "Protein-protein interactions play a central role in all cellular processes. Insight into their atomic architecture is therefore of paramount importance. Cryo-electron microscopy (cryo-EM) is capable of directly imaging large macromolecular complexes. Unfortunately, the resolution is usually not sufficient for a direct atomic interpretation. To overcome this, cryo-EM data are often combined with high-resolution atomic structures. However, current computational approaches typically do not include information from other experimental sources nor a proper physico-chemical description of the interfaces. Here we describe the integration of cryo-EM data into our data-driven docking program HADDOCK and its performance on a benchmark of 17 complexes. The approach is demonstrated on five systems using experimental cryo-EM data in the range of 8.5-21 Å resolution. For several cases, cryo-EM data are integrated with additional interface information, e.g. mutagenesis and hydroxyl radical footprinting data. The resulting models have high-quality interfaces, revealing novel details of the interactions.", "date": "2015-05-05T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Van Zundert G.C.P." }, { "name": "Melquiond A.S.J." }, { "name": "Bonvin A.M.J.J." } ], "journal": "Structure" } }, { "doi": "10.1111/febs.12771", "pmid": "24588898", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Integrative computational modeling of protein interactions", "abstract": "Protein interactions define the homeostatic state of the cell. Our ability to understand these interactions and their role in both health and disease is tied to our knowledge of the 3D atomic structure of the interacting partners and their complexes. Despite advances in experimental method of structure determination, the majority of known protein interactions are still missing an atomic structure. High-resolution methods such as X-ray crystallography and NMR spectroscopy struggle with the high-throughput demand, while low-resolution techniques such as cryo-electron microscopy or small-angle X-ray scattering provide data that are too coarse. Computational structure prediction of protein complexes, or docking, was first developed to complement experimental research and has since blossomed into an independent and lively field of research. Its most successful products are hybrid approaches that combine powerful algorithms with experimental data from various sources to generate high-resolution models of protein complexes. This minireview introduces the concept of docking and docking with the help of experimental data, compares and contrasts the available integrative docking methods, and provides a guide for the experimental researcher for what types of data and which particular software can be used to model a protein complex. © 2014 FEBS.", "date": "2014-01-01T00:00:00Z", "citationCount": 83, "authors": [ { "name": "Rodrigues J.P.G.L.M." }, { "name": "Bonvin A.M.J.J." } ], "journal": "FEBS Journal" } }, { "doi": "10.1016/j.yjsbx.2019.100006", "pmid": "32647812", "pmcid": "PMC7337051", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "West-Life: A Virtual Research Environment for structural biology", "abstract": "The West-Life project (https://about.west-life.eu/)is a Horizon 2020 project funded by the European Commission to provide data processing and data management services for the international community of structural biologists, and in particular to support integrative experimental approaches within the field of structural biology. It has developed enhancements to existing web services for structure solution and analysis, created new pipelines to link these services into more complex higher-level workflows, and added new data management facilities. Through this work it has striven to make the benefits of European e-Infrastructures more accessible to life-science researchers in general and structural biologists in particular.", "date": "2019-01-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Morris C." }, { "name": "Andreetto P." }, { "name": "Banci L." }, { "name": "Bonvin A.M.J.J." }, { "name": "Chojnowski G." }, { "name": "Cano L.D." }, { "name": "Carazo J.M." }, { "name": "Conesa P." }, { "name": "Daenke S." }, { "name": "Damaskos G." }, { "name": "Giachetti A." }, { "name": "Haley N.E.C." }, { "name": "Hekkelman M.L." }, { "name": "Heuser P." }, { "name": "Joosten R.P." }, { "name": "Kouril D." }, { "name": "Krenek A." }, { "name": "Kulhanek T." }, { "name": "Lamzin V.S." }, { "name": "Nadzirin N." }, { "name": "Perrakis A." }, { "name": "Rosato A." }, { "name": "Sanderson F." }, { "name": "Segura J." }, { "name": "Schaarschmidt J." }, { "name": "Sobolev E." }, { "name": "Traldi S." }, { "name": "Trellet M.E." }, { "name": "Velankar S." }, { "name": "Verlato M." }, { "name": "Winn M." } ], "journal": "Journal of Structural Biology: X" } }, { "doi": "10.1007/s10723-012-9246-z", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "WeNMR: Structural Biology on the Grid", "abstract": "The WeNMR (http://www. wenmr. eu) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI). © 2012 The Author(s).", "date": "2012-12-01T00:00:00Z", "citationCount": 163, "authors": [ { "name": "Wassenaar T.A." }, { "name": "van Dijk M." }, { "name": "Loureiro-Ferreira N." }, { "name": "van der Schot G." }, { "name": "de Vries S.J." }, { "name": "Schmitz C." }, { "name": "van der Zwan J." }, { "name": "Boelens R." }, { "name": "Giachetti A." }, { "name": "Ferella L." }, { "name": "Rosato A." }, { "name": "Bertini I." }, { "name": "Herrmann T." }, { "name": "Jonker H.R.A." }, { "name": "Bagaria A." }, { "name": "Jaravine V." }, { "name": "Guntert P." }, { "name": "Schwalbe H." }, { "name": "Vranken W.F." }, { "name": "Doreleijers J.F." }, { "name": "Vriend G." }, { "name": "Vuister G.W." }, { "name": "Franke D." }, { "name": "Kikhney A." }, { "name": "Svergun D.I." }, { "name": "Fogh R.H." }, { "name": "Ionides J." }, { "name": "Laue E.D." }, { "name": "Spronk C." }, { "name": "Jurksa S." }, { "name": "Verlato M." }, { "name": "Badoer S." }, { "name": "Dal Pra S." }, { "name": "Mazzucato M." }, { "name": "Frizziero E." }, { "name": "Bonvin A.M.J.J." } ], "journal": "Journal of Grid Computing" } }, { "doi": "10.1038/nprot.2010.32", "pmid": "20431534", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The HADDOCK web server for data-driven biomolecular docking", "abstract": "Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for a wide range of experimental data. Here we present the HADDOC K web server protocol, facilitating the modeling of biomolecular complexes for a wide community. The main web interface is user-friendly, requiring only the structures of the individual components and a list of interacting residues as input. Additional web interfaces allow the more advanced user to exploit the full range of experimental data supported by HADDOC K and to customize the docking process. The HADDOC K server has access to the resources of a dedicated cluster and of the e-NMR GRID infrastructure. Therefore, a typical docking run takes only a few minutes to prepare and a few hours to complete. © 2010 Nature Publishing Group.", "date": "2010-04-15T00:00:00Z", "citationCount": 1122, "authors": [ { "name": "De Vries S.J." }, { "name": "Van Dijk M." }, { "name": "Bonvin A.M.J.J." } ], "journal": "Nature Protocols" } } ], "credit": [ { "name": "University of Utrecht", "email": null, "url": "http://www.uu.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Bonvin Lab", "email": "a.m.j.j.bonvin@uu.nl", "url": "http://www.bonvinlab.org", "orcidid": "http://orcid.org/0000-0001-7369-1322", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer", "Primary contact", "Maintainer", "Provider", "Support" ], "note": null }, { "name": "EGI", "email": null, "url": "https://www.egi.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, West-Life VRE, grant no. 675858", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, INDICO-DataCloud, grant no. 653549", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, EGI-Engage, grant no. 654142", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, BioExcel, grant no. 675728", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Netherlands Organization for Scientific Research (NWO), VICI grant no. 700.96.442", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "Netherlands Organization for Scientific Research (NWO) , TOP-PUNT grant no. 718.015.001", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, BioExcel, grant no. 823830", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null }, { "name": "European H2020 e-Infrastructure grant, EOSC-Hub, grant no.777536", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "owner": "a.m.j.j.bonvin@uu.nl", "additionDate": "2016-10-03T14:08:37Z", "lastUpdate": "2024-11-24T15:23:11.797426Z", "editPermission": { "type": "group", "authors": [ "jdianes" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }