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GET /api/t/?topic=%22Proteomics%22
{ "count": 2289, "next": "?page=2", "previous": null, "list": [ { "name": "fluspred", "description": "FluSPred(Flu Spread Prediction) is a machine learning based tool to predict the human associated Influenza A virus strains with the help of its protein and genome sequences,", "homepage": "https://webs.iiitd.edu.in/raghava/fluspred/index.html", "biotoolsID": "fluspred", "biotoolsCURIE": "biotools:fluspred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_0321", "term": "Protein structure validation" }, { "uri": "http://edamontology.org/operation_3935", "term": "Dimensionality reduction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://webs.iiitd.edu.in/raghava/fluspred/index.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://github.com/raghavagps/FluSPred", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://webs.iiitd.edu.in/raghava/fluspred/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1099/jgv.0.001802", "pmid": "36318663", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "In silico method for predicting infectious strains of influenza A virus from its genome and protein sequences", "abstract": "Influenza A is a contagious viral disease responsible for four pandemics in the past and a major public health concern. Being zoonotic in nature, the virus can cross the species barrier and transmit from wild aquatic bird reservoirs to humans via intermediate hosts. In this study, we have developed a computational method for the prediction of human-associated and nonhuman-associated influenza A virus sequences. The models were trained and validated on proteins and genome sequences of influenza A virus. Firstly, we have developed prediction models for 15 types of influenza A proteins using composition-based and one-hot-encoding features. We have achieved a highest AUC of 0.98 for HA protein on a validation dataset using dipeptide composition-based features. Of note, we obtained a maximum AUC of 0.99 using one-hot-encoding features for protein-based models on a validation dataset. Secondly, we built models using whole genome sequences which achieved an AUC of 0.98 on a validation dataset. In addition, we showed that our method outperforms a similarity-based approach (i.e., blast) on the same validation dataset. Finally, we integrated our best models into a user-friendly web server ‘FluSPred’ (https://webs.iiitd.edu.in/raghava/fluspred/index.html) and a standalone version (https://github.com/raghavagps/FluSPred) for the prediction of human-associated/non-human-associated influenza A virus strains.", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Roy T." }, { "name": "Sharma K." }, { "name": "Dhall A." }, { "name": "Patiyal S." }, { "name": "Raghava G.P.S." } ], "journal": "Journal of General Virology" } } ], "credit": [ { "name": "Dr Gajendra P.S. Raghava", "email": null, "url": "https://webs.iiitd.edu.in/raghava/fluspred/index.html", "orcidid": "http://orcid.org/0000-0002-8902-2876", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sumeet Patiyal", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-1358-292X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Trinita Roy", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-2049-1391", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Khushal Sharma", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-6993-5408", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Anjali Dhall", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-0400-2084", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "raghavagps", "additionDate": "2022-10-03T09:24:57.447429Z", "lastUpdate": "2024-07-24T10:23:20.804894Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProNet DB", "description": "Proteome-wise database for protein surface property representations and RNA-binding profiles.", "homepage": "https://proj.cse.cuhk.edu.hk/aihlab/pronet/", "biotoolsID": "pronet_db", "biotoolsCURIE": "biotools:pronet_db", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3901", "term": "RNA-binding protein prediction" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" }, { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_3902", "term": "RNA binding site prediction" }, { "uri": "http://edamontology.org/operation_0387", "term": "Molecular surface calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://proj.cse.cuhk.edu.hk/aihlab/pronet/#/services", "type": [ "Other" ], "note": null }, { "url": "https://proj.cse.cuhk.edu.hk/aihlab/pronet/#/Home", "type": [ "Other" ], "note": null }, { "url": "https://github.com/jxmelody/PronetProcess", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/database/baae012", "pmid": "38557634", "pmcid": "PMC10984565", "type": [], "version": null, "note": null, "metadata": { "title": "ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles", "abstract": "The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures poses a significant challenge for computational biology in leveraging structural information and accurate representation of protein surface properties. Recently, AlphaFold2 released the comprehensive proteomes of various species, and protein surface property representation plays a crucial role in protein-molecule interaction predictions, including those involving proteins, nucleic acids and compounds. Here, we proposed the first extensive database, namely ProNet DB, that integrates multiple protein surface representations and RNA-binding landscape for 326 175 protein structures. This collection encompasses the 16 model organism proteomes from the AlphaFold Protein Structure Database and experimentally validated structures from the Protein Data Bank. For each protein, ProNet DB provides access to the original protein structures along with the detailed surface property representations encompassing hydrophobicity, charge distribution and hydrogen bonding potential as well as interactive fea-tures such as the interacting face and RNA-binding sites and preferences. To facilitate an intuitive interpretation of these properties and the RNA-binding landscape, ProNet DB incorporates visualization tools like Mol*and an Online 3D Viewer, allowing for the direct observation and analysis of these representations on protein surfaces. The availability of pre-computed features enables instantaneous access for users, signif-icantly advancing computational biology research in areas such as molecular mechanism elucidation, geometry-based drug discovery and the development of novel therapeutic approaches.", "date": "2024-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wei J." }, { "name": "Xiao J." }, { "name": "Chen S." }, { "name": "Zong L." }, { "name": "Gao X." }, { "name": "Li Y." } ], "journal": "Database" } } ], "credit": [ { "name": "Xin Gao", "email": "xin.gao@kaust.edu.sa", "url": null, "orcidid": "https://orcid.org/0000-0002-7108-3574", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Yu Li", "email": "liyu@cse.cuhk.edu.hk", "url": null, "orcidid": "https://orcid.org/0000-0002-3664-6722", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-07-18T11:20:28.077242Z", "lastUpdate": "2024-07-18T11:20:28.079611Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "OpenChrom", "description": "Open source tool for mass spectrometry and chromatography.", "homepage": "https://www.openchrom.net/", "biotoolsID": "openchrom", "biotoolsCURIE": "biotools:openchrom", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3203", "term": "Chromatogram visualisation" }, { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_1637", "term": "dat" }, { "uri": "http://edamontology.org/format_3712", "term": "Thermo RAW" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3650", "term": "netCDF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3650", "term": "netCDF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] }, { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/openchrom/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://sourceforge.net/p/openchrom/wiki/Home/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": null, "pmid": "20673335", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "OpenChrom: A cross-platform open source software for the mass spectrometric analysis of chromatographic data", "abstract": "Background: Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform.Results: This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported.Conclusions: OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at http://www.openchrom.net. © 2010 Wenig and Odermatt; licensee BioMed Central Ltd.", "date": "2010-07-30T00:00:00Z", "citationCount": 87, "authors": [ { "name": "Wenig P." }, { "name": "Odermatt J." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Philip Wenig", "email": "philip.wenig@gmx.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "community": null, "owner": "msutils_import", "additionDate": "2017-01-17T14:50:39Z", "lastUpdate": "2024-07-18T09:53:49.771511Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "Mailaender" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Expasy", "description": "Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools, supporting a range of life science and clinical research domains.", "homepage": "https://www.expasy.org/", "biotoolsID": "expasy", "biotoolsCURIE": "biotools:expasy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0957", "term": "Database metadata" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0958", "term": "Tool metadata" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3056", "term": "Population genetics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.expasy.org/about", "type": [ "General" ], "note": null }, { "url": "https://www.expasy.org/terms-of-use", "type": [ "Terms of use" ], "note": null } ], "publication": [ { "doi": null, "pmid": "12824418", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ExPASy: The proteomics server for in-depth protein knowledge and analysis", "abstract": "The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.", "date": "2003-07-01T00:00:00Z", "citationCount": 3943, "authors": [ { "name": "Gasteiger E." }, { "name": "Gattiker A." }, { "name": "Hoogland C." }, { "name": "Ivanyi I." }, { "name": "Appel R.D." }, { "name": "Bairoch A." } ], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "22661580", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ExPASy: SIB bioinformatics resource portal", "abstract": "ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 1633, "authors": [ { "name": "Artimo P." }, { "name": "Jonnalagedda M." }, { "name": "Arnold K." }, { "name": "Baratin D." }, { "name": "Csardi G." }, { "name": "De Castro E." }, { "name": "Duvaud S." }, { "name": "Flegel V." }, { "name": "Fortier A." }, { "name": "Gasteiger E." }, { "name": "Grosdidier A." }, { "name": "Hernandez C." }, { "name": "Ioannidis V." }, { "name": "Kuznetsov D." }, { "name": "Liechti R." }, { "name": "Moretti S." }, { "name": "Mostaguir K." }, { "name": "Redaschi N." }, { "name": "Rossier G." }, { "name": "Xenarios I." }, { "name": "Stockinger H." } ], "journal": "Nucleic Acids Research" } }, { "doi": null, "pmid": "8073505", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server", "abstract": "", "date": "1994-01-01T00:00:00Z", "citationCount": 520, "authors": [ { "name": "Appel R.D." }, { "name": "Bairoch A." }, { "name": "Hochstrasser D.F." } ], "journal": "Trends in Biochemical Sciences" } }, { "doi": null, "pmid": "33849055", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users", "abstract": "The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for the storage, analysis and interpretation of biological data. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. In 2020, Expasy was redesigned through a user-centric approach, known as User-Centred Design (UCD), whose aim is to create user interfaces that are easy-to-use, efficient and targeting the intended community. This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. In total, around 50 people were actively involved, including internal stakeholders and end-users. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources.", "date": "2021-07-02T00:00:00Z", "citationCount": 348, "authors": [ { "name": "Duvaud S." }, { "name": "Gabella C." }, { "name": "Lisacek F." }, { "name": "Stockinger H." }, { "name": "Ioannidis V." }, { "name": "Durinx C." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": "helpdesk@expasy.org", "url": null, "orcidid": null, "gridid": null, "rorid": "002n09z45", "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "community": null, "owner": "hstockin", "additionDate": "2017-05-01T14:07:25Z", "lastUpdate": "2024-07-10T13:58:59.242523Z", "editPermission": { "type": "group", "authors": [ "hstockin", "proteomics.bio.tools", "mzahn" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSFragger", "description": "A database search tool for performing mass spectometry data similarity comparisons. For that it uses a fragment ion indexing method.", "homepage": "http://www.nesvilab.org/software", "biotoolsID": "msfragger", "biotoolsCURIE": "biotools:msfragger", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3712", "term": "Thermo RAW" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [], "language": [ "Java" ], "license": "Other", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.nesvilab.org/software", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/nmeth.4256", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MSFragger: Ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics", "abstract": "There is a need to better understand and handle the 'dark matter' of proteomics-the vast diversity of post-translational and chemical modifications that are unaccounted in a typical mass spectrometry-based analysis and thus remain unidentified. We present a fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools. Using several large proteomic data sets, we demonstrate how MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in modification rates across experimental samples and conditions. We further illustrate its utility using protein-RNA cross-linked peptide data and using affinity purification experiments where we observe, on average, a 300% increase in the number of identified spectra for enriched proteins. We also discuss the benefits of open searching for improved false discovery rate estimation in proteomics.", "date": "2017-04-27T00:00:00Z", "citationCount": 877, "authors": [ { "name": "Kong A.T." }, { "name": "Leprevost F.V." }, { "name": "Avtonomov D.M." }, { "name": "Mellacheruvu D." }, { "name": "Nesvizhskii A.I." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Alexey Nesvizhskii", "email": "nesvi@umich.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "ELIXIR-EE", "additionDate": "2018-06-11T09:48:30Z", "lastUpdate": "2024-07-10T10:06:37.289299Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "n.m.palmblad@lumc.nl" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PTXQC", "description": "PTXQC is a quality control pipeline for proteomics results generated by MaxQuant.", "homepage": "https://github.com/cbielow/PTXQC", "biotoolsID": "ptxqc", "biotoolsCURIE": "biotools:ptxqc", "version": [ "1.1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1021/acs.jproteome.5b00780", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Proteomics Quality Control: Quality Control Software for MaxQuant Results", "abstract": "Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA) capable of detecting measurement bias, verifying consistency, and avoiding propagation of error is paramount for instrument operators and scientists in charge of downstream analysis. We have developed an R-based QC pipeline called Proteomics Quality Control (PTXQC) for bottom-up LC-MS data generated by the MaxQuant1 software pipeline. PTXQC creates a QC report containing a comprehensive and powerful set of QC metrics, augmented with automated scoring functions. The automated scores are collated to create an overview heatmap at the beginning of the report, giving valuable guidance also to nonspecialists. Our software supports a wide range of experimental designs, including stable isotope labeling by amino acids in cell culture (SILAC), tandem mass tags (TMT), and label-free data. Furthermore, we introduce new metrics to score MaxQuant's Match-between-runs (MBR) functionality by which peptide identifications can be transferred across Raw files based on accurate retention time and m/z. Last but not least, PTXQC is easy to install and use and represents the first QC software capable of processing MaxQuant result tables. PTXQC is freely available at https://github.com/cbielow/PTXQC.", "date": "2016-03-04T00:00:00Z", "citationCount": 118, "authors": [ { "name": "Bielow C." }, { "name": "Mastrobuoni G." }, { "name": "Kempa S." } ], "journal": "Journal of Proteome Research" } } ], "credit": [], "community": null, "owner": "n.m.palmblad@lumc.nl", "additionDate": "2024-06-20T15:23:46.935418Z", "lastUpdate": "2024-06-20T15:23:46.941833Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "xMarkerFinder", "description": "Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder.", "homepage": "https://www.biosino.org/xmarkerfinder/", "biotoolsID": "xmarkerfinder", "biotoolsCURIE": "biotools:xmarkerfinder", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" }, { "uri": "http://edamontology.org/operation_3435", "term": "Standardisation and normalisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3360", "term": "Biomarkers" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3941", "term": "Metatranscriptomics" }, { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/tjcadd2020/xMarkerFinder", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/s41596-024-00999-9", "pmid": "38745111", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder", "abstract": "Microbial signatures have emerged as promising biomarkers for disease diagnostics and prognostics, yet their variability across different studies calls for a standardized approach to biomarker research. Therefore, we introduce xMarkerFinder, a four-stage computational framework for microbial biomarker identification with comprehensive validations from cross-cohort datasets, including differential signature identification, model construction, model validation and biomarker interpretation. xMarkerFinder enables the identification and validation of reproducible biomarkers for cross-cohort studies, along with the establishment of classification models and potential microbiome-induced mechanisms. Originally developed for gut microbiome research, xMarkerFinder’s adaptable design makes it applicable to various microbial habitats and data types. Distinct from existing biomarker research tools that typically concentrate on a singular aspect, xMarkerFinder uniquely incorporates a sophisticated feature selection process, specifically designed to address the heterogeneity between different cohorts, extensive internal and external validations, and detailed specificity assessments. Execution time varies depending on the sample size, selected algorithm and computational resource. Accessible via GitHub (https://github.com/tjcadd2020/xMarkerFinder), xMarkerFinder supports users with diverse expertise levels through different execution options, including step-to-step scripts with detailed tutorials and frequently asked questions, a single-command execution script, a ready-to-use Docker image and a user-friendly web server (https://www.biosino.org/xmarkerfinder).", "date": "2024-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Gao W." }, { "name": "Lin W." }, { "name": "Li Q." }, { "name": "Chen W." }, { "name": "Yin W." }, { "name": "Zhu X." }, { "name": "Gao S." }, { "name": "Liu L." }, { "name": "Li W." }, { "name": "Wu D." }, { "name": "Zhang G." }, { "name": "Zhu R." }, { "name": "Jiao N." } ], "journal": "Nature Protocols" } } ], "credit": [ { "name": "Na Jiao", "email": "najiao@fudan.edu.cn", "url": null, "orcidid": "http://orcid.org/0000-0003-3976-6313", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-06-19T08:45:02.037038Z", "lastUpdate": "2024-06-19T08:45:02.040216Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "FlexStat", "description": "Web-based interface that extracts DEPs through combinatory analysis.", "homepage": "https://jglab.shinyapps.io/flexstatv1-pipeline-only/", "biotoolsID": "flexstat", "biotoolsCURIE": "biotools:flexstat", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/kts-desilva/FlexStat/tree/main", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/bioadv/vbae056", "pmid": "38681522", "pmcid": "PMC11055397", "type": [], "version": null, "note": null, "metadata": { "title": "FlexStat: combinatory differentially expressed protein extraction", "abstract": "Motivation: Mass spectrometry-based system proteomics allows identification of dysregulated protein hubs and associated disease-related features. Obtaining differentially expressed proteins (DEPs) is the most important step of downstream bioinformatics analysis. However, the extraction of statistically significant DEPs from datasets with multiple experimental conditions or disease types through currently available tools remains a laborious task. More often such an analysis requires considerable bioinformatics expertise, making it inaccessible to researchers with limited computational analytics experience. Results: To uncover the differences among the many conditions within the data in a user-friendly manner, here we introduce FlexStat, a web-based interface that extracts DEPs through combinatory analysis. This tool accepts a protein expression matrix as input and systematically generates DEP results for every conceivable combination of various experimental conditions or disease types. FlexStat includes a suite of robust statistical tools for data preprocessing, in addition to DEP extraction, and publication-ready visualization, which are built on established R scientific libraries in an automated manner. This analytics suite was validated in diverse public proteomic datasets to showcase its high performance of rapid and simultaneous pairwise comparisons of comprehensive datasets. Availability and implementation: FlexStat is implemented in R and is freely available at https://jglab.shinyapps.io/flexstatv1-pipeline-only/. The source code is accessible at https://github.com/kts-desilva/FlexStat/tree/main.", "date": "2024-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "De Silva S." }, { "name": "Alli-Shaik A." }, { "name": "Gunaratne J." } ], "journal": "Bioinformatics Advances" } } ], "credit": [ { "name": "Jayantha Gunaratne", "email": "jayanthag@imcb.a-star.edu.sg", "url": null, "orcidid": "https://orcid.org/0000-0002-5377-6537", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Senuri De Silva", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Asfa Alli-Shaik", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-06-19T08:01:53.557371Z", "lastUpdate": "2024-06-19T08:01:53.559495Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "CLIPPER 2.0", "description": "Peptide level annotation and data analysis for positional proteomics.", "homepage": "https://github.com/UadKLab/CLIPPER-2.0", "biotoolsID": "clipper_2.0", "biotoolsCURIE": "biotools:clipper_2.0", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2939", "term": "Principal component visualisation" }, { "uri": "http://edamontology.org/operation_3891", "term": "Essential dynamics" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/j.mcpro.2024.100781", "pmid": "38703894", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Konstantinos Kalogeropoulos", "email": "konka@dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Aleksander Moldt Haack", "email": "alemol@dtu.dk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-06-19T07:56:22.584913Z", "lastUpdate": "2024-06-19T07:56:22.587526Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "OmicNavigator", "description": "Open-source software for the exploration, visualization, and archival of omic studies.", "homepage": "https://github.com/abbvie-external/OmicNavigator", "biotoolsID": "omicnavigator", "biotoolsCURIE": "biotools:omicnavigator", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [ "R" ], "license": "LAL-1.2", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s12859-024-05743-4", "pmid": "38658834", "pmcid": "PMC11040775", "type": [], "version": null, "note": null, "metadata": { "title": "OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies", "abstract": "Background: The results of high-throughput biology (‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features. Results: We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access. Conclusions: OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator", "date": "2024-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Ernst T.R." }, { "name": "Blischak J.D." }, { "name": "Nordlund P." }, { "name": "Dalen J." }, { "name": "Moore J." }, { "name": "Bhamidipati A." }, { "name": "Dwivedi P." }, { "name": "LoGrasso J." }, { "name": "Curado M.R." }, { "name": "Engelmann B.W." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Brett Warren Engelmann", "email": "brett.engelmann@abbvie.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Terrence R. Ernst", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2024-06-19T07:51:07.799272Z", "lastUpdate": "2024-06-19T07:51:07.801495Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }