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GET /api/t/?inputDataType=%22Protein+sequence%22
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"10.24072/pcjournal.250", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes", "abstract": "Complex cellular functions are usually encoded by a set of genes in one or a few orga-nized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular mod-els: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder.", "date": "2023-01-01T00:00:00Z", "citationCount": 43, "authors": [ { "name": "Neron B." }, { "name": "Denise R." }, { "name": "Coluzzi C." }, { "name": "Touchon M." }, { "name": "Rocha E.P.C." }, { "name": "Abby S.S." } ], "journal": "Peer Community Journal" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "0495fxg12", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Microbial Evolutionary Genomics Unit", "email": null, "url": "https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics HUB", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Eduardo P.C. Rocha", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7704-822X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sophie Abby", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-5231-3346", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Bertrand Néron", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-0220-0482", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "bneron", "additionDate": "2025-08-07T10:25:22.118390Z", "lastUpdate": "2025-08-11T12:14:42.322020Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "EukCC", "description": "EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.", "homepage": "https://github.com/EBI-Metagenomics/EukCC", "biotoolsID": "eukcc", "biotoolsCURIE": "biotools:eukcc", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3180", "term": "Sequence assembly validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2955", "term": "Sequence report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/s13059-020-02155-4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC", "abstract": "Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.", "date": "2020-09-10T00:00:00Z", "citationCount": 70, "authors": [ { "name": "Saary P." }, { "name": "Mitchell A.L." }, { "name": "Finn R.D." } ], "journal": "Genome Biology" } } ], "credit": [], "owner": "m.bernt", "additionDate": "2025-07-24T07:14:51.692628Z", "lastUpdate": "2025-07-24T07:14:51.694965Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UniversalMer", "description": "UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.", "homepage": "https://ugrammer.github.io", "biotoolsID": "UniversalMer", "biotoolsCURIE": "biotools:UniversalMer", "version": [ "2.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3472", "term": "k-mer counting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] }, { "data": { "uri": "http://edamontology.org/data_3495", "term": "RNA sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1266", "term": "Base word frequencies table" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1265", "term": "Base frequencies table" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [ "C++", "C" ], "license": "Freeware", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://sourceforge.net/projects/universal-mer/", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "https://sourceforge.net/projects/universal-mer/", "type": "Command-line specification", "note": null, "version": "2.0" } ], "documentation": [], "publication": [], "credit": [], "owner": "Ugrammer", "additionDate": "2025-07-14T08:21:28.942611Z", "lastUpdate": "2025-07-14T08:21:28.944946Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProteinPrompt", "description": "A webserver for predicting protein-protein interactions.", "homepage": "http://proteinformatics.org/ProteinPrompt", "biotoolsID": "proteinprompt", "biotoolsCURIE": "biotools:proteinprompt", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2464", "term": "Protein-protein binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3957", "term": "Protein interaction experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitlab.hzdr.de/proteinprompt/ProteinPrompt", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1101/2021.09.03.458859", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "René Staritzbichler", "email": "rene.staritzbichler@medizin.uni-leipzig.de", "url": null, "orcidid": "https://orcid.org/0000-0002-6719-2997", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Peter W. Hildebrand", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0063-1104", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Sebastian Canzler", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7935-9582", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Markus Fischer", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "David Ulbricht", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Nikola Ristic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-02-07T23:41:36.733362Z", "lastUpdate": "2025-07-02T08:39:17.251278Z", "editPermission": { "type": "group", "authors": [ "andleeb" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "DeepSig", "description": "Prediction of secretory signal peptides in protein sequences", "homepage": "https://busca.biocomp.unibo.it/deepsig/", "biotoolsID": "deepsig", "biotoolsCURIE": "biotools:deepsig", "version": [ "1.2.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0418", "term": "Protein signal peptide detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3028", "term": "Taxonomy" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python", "C++" ], "license": "GPL-3.0", "collectionID": [ "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": "Source code", "note": null, "version": "1.2.5" }, { "url": "https://hub.docker.com/r/bolognabiocomp/deepsig", "type": "Container file", "note": null, "version": "1.2.5" } ], "documentation": [ { "url": "https://github.com/BolognaBiocomp/deepsig", "type": [ "Command-line options" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx818", "pmid": "29280997", "pmcid": "PMC5946842", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "DeepSig: Deep learning improves signal peptide detection in proteins", "abstract": "Motivation The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website.", "date": "2018-05-15T00:00:00Z", "citationCount": 96, "authors": [ { "name": "Savojardo C." }, { "name": "Martelli P.L." }, { "name": "Fariselli P." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Castrense Savojardo", "email": "castrense.savojardo2@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": "http://biocomp.unibo.it", "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2018-05-28T14:50:09Z", "lastUpdate": "2025-06-19T11:55:09.017105Z", "editPermission": { "type": "group", "authors": [ "savo", "ELIXIR-ITA-BOLOGNA" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "OMA", "description": "Project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind.", "homepage": "http://omabrowser.org/oma/home/", "biotoolsID": "oma", "biotoolsCURIE": "biotools:oma", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3671", "term": "Text" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [], "note": "orthology prediction and paralogy OMA group", "cmd": null } ], "toolType": [ "Web application", "Database portal", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3299", "term": "Evolutionary biology" }, { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://omabrowser.org/oma/about/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gku1158", "pmid": "25399418", "pmcid": "PMC4383958", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The OMA orthology database in 2015: Function predictions, better plant support, synteny view and other improvements", "abstract": "The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes). In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction. OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.", "date": "2015-01-28T00:00:00Z", "citationCount": 160, "authors": [ { "name": "Altenhoff A.M." }, { "name": "Sunca N." }, { "name": "Glover N." }, { "name": "Train C.-M." }, { "name": "Sueki A." }, { "name": "Pilizota I." }, { "name": "Gori K." }, { "name": "Tomiczek B." }, { "name": "Muller S." }, { "name": "Redestig H." }, { "name": "Gonnet G.H." }, { "name": "Dessimoz C." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkad1020", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "OMA or tholog y in 2024: impro v ed prokary ot e co v erãg e,ãncestralãnd extant GO enrichment,ã revamped synteny viewerãnd more in the OMA Ecosystem", "abstract": "In this update paper, we present the latest de v elopments in the OMA browser knowledgebase, whichãims to provide high-quality orthology inferencesãnd facilitate the study of gene families, genomesãnd their evolution. First, we discuss theãddition of new species in the database, particularlyãn expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pagesãndãn Ancestral Gene Order vie w er,ãllo wing users to e xplore the e v olutionar y histor yãnd gene content ofãncestral genomes. Weãlso introduceã re vãmped L ocal Synten y Vie w er to compare genomic neighborhoodsãcross both e xtantãndãncestral genomes. Hierarchical Orthologous Groups (H O Gs)ãre nowãnnotated with Gene Ontologyãnnotations,ãnd users can easily perform extant orãncestral GO enrichments. Finally, we recap new tools in the OMA Ecosystem, including OMAmer for proteome mapping, OMArk for proteome qualityãssessment, OMAMO for model organism selectionãnd Read2Tree for phylogenetic species tree construction from reads. These new features provide exciting opportunities for orthologyãnalysisãnd comparative genomics. OMA isãccessibleãt https://omabrowser.org .", "date": "2024-01-05T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Altenhoff A.M." }, { "name": "Vesztrocy A.W." }, { "name": "Bernard C." }, { "name": "Train C.-M." }, { "name": "Nicheperovich A." }, { "name": "Banos S.P." }, { "name": "Julca I." }, { "name": "Moi D." }, { "name": "Nevers Y." }, { "name": "Majidian S." }, { "name": "Dessimoz C." }, { "name": "Glover N.M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkaa1007", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "OMA orthology in 2021: Website overhaul, conserved isoforms, ancestral gene order and more", "abstract": "OMA is an established resource to elucidate evolutionary relationships among genes from currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise orthologs, functional annotations, local and global gene order conservation (synteny) information, among many other functions. This update paper describes the reorganisation of the database into gene-, group- and genome-centric pages. Other new and improved features are detailed, such as reporting of the evolutionarily best conserved isoforms of alternatively spliced genes, the inferred local order of ancestral genes, phylogenetic profiling, better cross-references, fast genome mapping, semantic data sharing via RDF, as well as a special coronavirus OMA with 119 viruses from the Nidovirales order, including SARS-CoV-2, the agent of the COVID-19 pandemic. We conclude with improvements to the documentation of the resource through primers, tutorials and short videos. OMA is accessible at https://omabrowser.org.", "date": "2021-01-08T00:00:00Z", "citationCount": 135, "authors": [ { "name": "Altenhoff A.M." }, { "name": "Train C.-M." }, { "name": "Gilbert K.J." }, { "name": "Mediratta I." }, { "name": "de Farias T.M." }, { "name": "Moi D." }, { "name": "Nevers Y." }, { "name": "Radoykova H.-S." }, { "name": "Rossier V." }, { "name": "Vesztrocy A.W." }, { "name": "Glover N.M." }, { "name": "Dessimoz C." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1019", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The OMA orthology database in 2018: Retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces", "abstract": "The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.", "date": "2018-01-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Altenhoff A.M." }, { "name": "Glover N.M." }, { "name": "Train C.-M." }, { "name": "Kaleb K." }, { "name": "Warwick Vesztrocy A." }, { "name": "Dylus D." }, { "name": "De Farias T.M." }, { "name": "Zile K." }, { "name": "Stevenson C." }, { "name": "Long J." }, { "name": "Redestig H." }, { "name": "Gonnet G.H." }, { "name": "Dessimoz C." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "contact@omabrowser.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Christophe Dessimoz", "email": "Christophe.Dessimoz@unil.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "adrian.altenhoff", "additionDate": "2016-06-24T11:36:59Z", "lastUpdate": "2025-06-03T08:27:37.764262Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioSurfDB", "description": "BioSurfDB is a online database for biodegradation and biosurfactants.", "homepage": "https://www.biosurfdb.org", "biotoolsID": "biosurfdb", "biotoolsCURIE": "biotools:biosurfdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1385", "term": "Hybrid sequence alignment" }, "format": [] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0349", "term": "Sequence database search (by property)" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_1026", "term": "Gene symbol" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1027", "term": "Gene ID (NCBI)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3297", "term": "Biotechnology" }, { "uri": "http://edamontology.org/topic_3301", "term": "Microbiology" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/database/bav033", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation studies", "abstract": "Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria. Many research studies are making available genomic data from unknown organisms obtained from metagenomics analysis of oil-contaminated environmental samples. These new datasets are presently demanding the development of new tools and data repositories tailored for the biological analysis in a context of bioremediation data analysis. This work presents BioSurfDB, www.biosurfdb.org, a curated relational information system integrating data from: (i) metagenomes; (ii) organisms; (iii) biodegradation relevant genes; proteins and their metabolic pathways; (iv) bioremediation experiments results, with specific pollutants treatment efficiencies by surfactant producing organisms; and (v) a biosurfactant-curated list, grouped by producing organism, surfactant name, class and reference. The main goal of this repository is to gather information on the characterization of biological compounds and mechanisms involved in biosurfactant production and/or biodegradation and make it available in a curated way and associated with a number of computational tools to support studies of genomic and metagenomic data.", "date": "2015-01-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Oliveira J.S." }, { "name": "Araujo W." }, { "name": "Sales A.I.L." }, { "name": "De Brito Guerra A." }, { "name": "Da Silva Araujo S.C." }, { "name": "De Vasconcelos A.T.R." }, { "name": "Agnez-Lima L.F." }, { "name": "Freitas A.T." } ], "journal": "Database" } } ], "credit": [ { "name": "Jorge S. Oliveira", "email": "jorge.oliveira@tecnico.ulisboa.pt", "url": "https://web.tecnico.ulisboa.pt/jorge.oliveira/", "orcidid": "https://orcid.org/0000-0001-6425-2176", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Teresa Freitas", "email": "ana.freitas@tecnico.ulisboa.pt", "url": null, "orcidid": "http://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Ana Tereza Ribeiro de Vasconcelos", "email": "atrv@lncc.br", "url": null, "orcidid": "http://orcid.org/0000-0002-4632-2086", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Lucymara Fassarella Agnez-Lima", "email": "lucymara.agnez@ufrn.br", "url": null, "orcidid": "http://orcid.org/0000-0003-0642-3162", "gridid": null, "rorid": null, 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As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The prolfquapp addresses this challenge by providing a command-line interface that simplifies DEA, making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems. Prolfquapp streamlines data processing and result visualization by generating dynamic HTML reports that facilitate the exploration of differential expression results. These reports allow for investigating complex experiments, such as those involving repeated measurements or multiple explanatory variables. Additionally, prolfquapp supports various output formats, including XLSX files, SummarizedExperiment objects and rank files, for further interactive analysis using spreadsheet software, the exploreDE Shiny application, or gene set enrichment analysis software, respectively. By leveraging advanced statistical models from the prolfqua R package, prolfquapp offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs.", "date": "2025-02-07T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Wolski W.E." }, { "name": "Grossmann J." }, { "name": "Schwarz L." }, { "name": "Leary P." }, { "name": "Turker C." }, { "name": "Nanni P." }, { "name": "Schlapbach R." }, { "name": "Panse C." } ], "journal": "Journal of Proteome Research" } } ], "credit": [], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2025-02-28T15:04:33.594183Z", "lastUpdate": "2025-03-28T10:18:25.715685Z", "editPermission": { "type": "group", "authors": [ "thatmariia" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PEP-FOLD4", "description": "PEP-FOLD4 is a fast and accurate structure prediction tool for peptides of up to 40 amino acids in aqueous solutions. Unlike many machine-learning approaches (e.g., AlphaFold2, TrRosetta, RaptorX), it integrates the Debye-Hückel formalism for charged side-chain interactions with a Mie potential for intramolecular forces. Based on a coarse-grained representation, PEP-FOLD4 performs competitively on well-structured peptides and shows significant improvements for poly-charged peptides, making it particularly useful for studying pH- and salt-dependent conformations.", "homepage": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4", "biotoolsID": "pep-fold4", "biotoolsCURIE": "biotools:pep-fold4", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_1475", "term": "PDB database entry format" } ] }, { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" } ], "operatingSystem": [], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [ { "url": "https://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD4", "type": [ "Service" ], "note": "Link to the PEP-FOLD4 web page service" } ], "download": [ { "url": "https://owncloud.rpbs.univ-paris-diderot.fr/owncloud/index.php/s/7NHDSJXiQA0V2zy", "type": "Source code", "note": "Source code and recipe for docker images allowing to run PEP-FOLD4 locally. All repository content is covered by a non-commercial license agreement and may be used for non-commercial and internal research purposes only.", "version": null } ], "documentation": [ { "url": "https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkad376", "pmid": "37166962", "pmcid": "PMC10320157", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PEP-FOLD4: A pH-dependent force field for peptide structure prediction in aqueous solution", "abstract": "Accurate and fast structure prediction of peptides of less 40 amino acids in aqueous solution has many biological applications, but their conformations are pH-and salt concentration-dependent. In this work, we present PEP-FOLD4 which goes one step beyond many machine-learning approaches, such as AlphaFold2, TrRosetta and RaptorX. Adding the Debye-Hueckel formalism for charged-charged side chain interactions to a Mie formalism for all intramolecular (backbone and side chain) interactions, PEP-FOLD4, based on a coarse-grained representation of the peptides, performs as well as machine-learning methods on well-structured peptides, but displays significant improvements for poly-charged peptides. PEP-FOLD4 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4. 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Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage’s receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. 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Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features and gene neighborhoods information to phylogeny, researchers need to prepare all the necessary data and combine them by hand, which is time-consuming and error-prone. Here, we present a new platform, TREND (tree-based exploration of neighborhoods and domains), which can perform all the necessary steps in automated fashion and put the derived information into phylogenomic context, thus making evolutionary based protein function analysis more efficient. A rich set of adjustable components allows a user to run the computational steps specific to his task. 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null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://huanglab.phys.hust.edu.cn/hsymdock/help.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky398", "pmid": "29846641", "pmcid": "PMC6030965", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "HSYMDOCK: A docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry", "abstract": "A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 101/420 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.", "date": "2018-07-02T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Yan Y." }, { "name": "Tao H." }, { "name": "Huang S.-Y." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "huanglab@hust.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-06-18T09:30:36Z", "lastUpdate": "2024-11-25T14:41:44.638481Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MobiDB-lite", "description": "MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions", "homepage": "http://protein.bio.unipd.it/mobidblite/", "biotoolsID": "mobidb-lite", "biotoolsCURIE": "biotools:mobidb-lite", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" } ], "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_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2548", "term": "Sequence feature table format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://protein.bio.unipd.it/download/", "type": "Software package", "note": null, "version": null } ], "documentation": [ { "url": "http://protein.bio.unipd.it/mobidblite/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btx015", "pmid": "28453683", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MobiDB-lite: Fast and highly specific consensus prediction of intrinsic disorder in proteins", "abstract": "Motivation: Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of many methods with similar performance at the single residue level, which have mostly not been optimized to predict long ID regions of size comparable to domains. Results: Here, we have focused on providing a single consensus-based prediction, MobiDB-lite, optimized for highly specific (i.e. few false positive) predictions of long disorder. The method uses eight different predictors to derive a consensus which is then filtered for spurious short predictions. Consensus prediction is shown to outperform the single methods when annotating long ID regions. MobiDB-lite can be useful in large-scale annotation scenarios and has indeed already been integrated in the MobiDB, DisProt and InterPro databases.", "date": "2017-05-01T00:00:00Z", "citationCount": 139, "authors": [ { "name": "Necci M." }, { "name": "Piovesan D." }, { "name": "Dosztanyi Z." }, { "name": "Tosatto S.C.E." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "University of Padua, Department of Biomedical Sciences, BioComputing UP lab", "email": null, "url": "http://protein.bio.unipd.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "ELIXIR-ITA-PADOVA", "email": null, "url": "http://elixir.bio.unipd.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Silvio C.E. Tosatto", "email": "silvio.tosatto@unipd.it", "url": "http://protein.bio.unipd.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-PADOVA", "additionDate": "2018-03-12T09:45:00Z", "lastUpdate": "2024-11-25T14:39:51.264257Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RosettaES", "description": "An automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3–5-Å resolution.", "homepage": "https://www.rosettacommons.org/", "biotoolsID": "rosettaes", "biotoolsCURIE": "biotools:rosettaes", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_2480", "term": "Structure analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1710", "term": "Structure image" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] }, { "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_0889", "term": "Structural profile" }, "format": [ { "uri": "http://edamontology.org/format_2032", "term": "Workflow format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0611", "term": "Electron microscopy" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.rosettacommons.org/docs/latest/release-notes", "type": "API specification", "note": null, "version": null } ], "documentation": [ { "url": "https://media.nature.com/original/nature-assets/nmeth/journal/v14/n8/extref/nmeth.4340-S2.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.4340", "pmid": "28628127", "pmcid": "PMC6009829", "type": [], "version": null, "note": null, "metadata": { "title": "RosettaES: A sampling strategy enabling automated interpretation of difficult cryo-EMmaps", "abstract": "Accurate atomic modeling of macromolecular structures into cryo-electron microscopy (cryo-EM) maps is a major challenge, as the moderate resolution makes accurate placement of atoms difficult. We present Rosetta enumerative sampling (RosettaES), an automated tool that uses a fragment-based sampling strategy for de novo model completion of macromolecular structures from cryo-EM density maps at 3-5-Å resolution. On a benchmark set of nine proteins, RosettaES was able to identify near-native conformations in 85% of segments. RosettaES was also used to determine models for three challenging macromolecular structures.", "date": "2017-07-28T00:00:00Z", "citationCount": 85, "authors": [ { "name": "Frenz B." }, { "name": "Walls A.C." }, { "name": "Egelman E.H." }, { "name": "Veesler D." }, { "name": "Di Maio F." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Frank Dimaio", "email": "dimaio@u.washington.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2018-06-04T16:46:37Z", "lastUpdate": "2024-11-25T14:37:56.751132Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }