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{ "count": 392, "next": "?page=2", "previous": null, "list": [ { "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, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Gil Poiares-Oliveira", "email": "gpo@biodata.pt", "url": "https://web.tecnico.ulisboa.pt/gil.oliveira", "orcidid": "https://orcid.org/0000-0003-4638-2879", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "ELIXIR-PT", "additionDate": "2025-04-29T17:07:56.642694Z", "lastUpdate": "2025-04-29T17:35:41.655075Z", "editPermission": { "type": "group", "authors": [ "gpo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "prolfquapp", "description": "A command-line tool for differential expression analysis in quantitative proteomics", "homepage": "https://github.com/prolfqua/prolfquapp", "biotoolsID": "prolfquapp", "biotoolsCURIE": "biotools:prolfquapp", "version": [ "0.1.6" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": "./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN\n# and again you run the version within the docker container with\n# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN" }, { "operation": [ { "uri": "http://edamontology.org/operation_2428", "term": "Validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0571", "term": "Expression data visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "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_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3508", "term": "PDF" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Mac", "Linux" ], "language": [ "R" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/prolfqua/prolfquapp", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/prolfqua/prolfquapp/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/prolfqua/prolfquapp/releases/tag/0.1.6", "type": "Downloads page", "note": null, "version": "0.1.6" } ], "documentation": [ { "url": "https://github.com/prolfqua/prolfquapp/blob/master/README.md", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.4c00911", "pmid": null, "pmcid": null, "type": [], "version": "0.0.6", "note": null, "metadata": { "title": "prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics", "abstract": "Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis (DEA) of proteins. 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": "INPS-MD", "description": "Predicting the impact of mutations on protein stability from sequence and structure.", "homepage": "http://inpsmd.biocomp.unibo.it", "biotoolsID": "inps-md", "biotoolsCURIE": "biotools:inps-md", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from sequence.", "cmd": null }, { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1008", "term": "Polypeptide chain ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1460", "term": "Protein structure" }, "format": [] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability from structure.", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://inpsmd.biocomp.unibo.it/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv291", "pmid": "25957347", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS: Predicting the impact of non-synonymous variations on protein stability from sequence", "abstract": "Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences. Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.", "date": "2015-02-06T00:00:00Z", "citationCount": 111, "authors": [ { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw192", "pmid": "27153629", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS-MD: A web server to predict stability of protein variants from sequence and structure", "abstract": "Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular mechanisms of human diseases and help in developing new drugs. Recently, we introduced INPS, a method suited to predict the effect of variations on protein stability from protein sequence and whose performance is competitive with the available state-of-the-art tools. Results: In this article, we describe INPS-MD (Impact of Non synonymous variations on Protein Stability-Multi-Dimension), a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits features derived from protein 3D structure. INPS3D scores with Pearson's correlation to experimental ΔΔG values of 0.58 in cross validation and of 0.72 on a blind test set. The sequence-based INPS scores slightly lower than the structure-based INPS3D and both on the same blind test sets well compare with the state-of-the-art methods.", "date": "2016-08-15T00:00:00Z", "citationCount": 189, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "https://www.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" ], "note": null }, { "name": "Piero Fariselli", "email": "piero.fariselli@unito.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Castrense Savojardo", "email": "savojard@biocomp.unibo.it", "url": "http://biocomp.unibo.it/savojard/", "orcidid": "https://orcid.org/0000-0002-7359-0633", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-05-04T15:36:53Z", "lastUpdate": "2025-03-19T15:01:04.207003Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo", "Pub2Tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DDGemb", "description": "Predicting the impact of mutations on protein stability from sequence using protein language models", "homepage": "https://ddgemb.biocomp.unibo.it", "biotoolsID": "ddgemb", "biotoolsCURIE": "biotools:ddgemb", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases", "3D-BioInfo" ], "link": [], "download": [], "documentation": [ { "url": "https://ddgemb.biocomp.unibo.it/help/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btaf019", "pmid": "39799516", "pmcid": "PMC11783275", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning", "abstract": "Motivation: The knowledge of protein stability upon residue variation is an important step for functional protein design and for understanding how protein variants can promote disease onset. Computational methods are important to complement experimental approaches and allow a fast screening of large datasets of variations. Results: In this work, we present DDGemb, a novel method combining protein language model embeddings and transformer architectures to predict protein ΔΔG upon both single- and multi-point variations. DDGemb has been trained on a high-quality dataset derived from literature and tested on available benchmark datasets of single- and multi-point variations. DDGemb performs at the state of the art in both single- and multi-point variations.", "date": "2025-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Savojardo C." }, { "name": "Manfredi M." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "https://www.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": [ "Maintainer", "Developer", "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2025-03-17T14:56:35.753220Z", "lastUpdate": "2025-03-17T15:08:51.796427Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "INPS", "description": "Predicting the impact of mutations on protein stability from sequence", "homepage": "https://inpsmd.biocomp.unibo.it", "biotoolsID": "inps", "biotoolsCURIE": "biotools:inps", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [] } ], "note": "Prediction of the impact of non-synonymous polymorphisms on protein stability", "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://inpsmd.biocomp.unibo.it/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv291", "pmid": "25957347", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS: Predicting the impact of non-synonymous variations on protein stability from sequence", "abstract": "Motivation: A tool for reliably predicting the impact of variations on protein stability is extremely important for both protein engineering and for understanding the effects of Mendelian and somatic mutations in the genome. Next Generation Sequencing studies are constantly increasing the number of protein sequences. Given the huge disproportion between protein sequences and structures, there is a need for tools suited to annotate the effect of mutations starting from protein sequence without relying on the structure. Here, we describe INPS, a novel approach for annotating the effect of non-synonymous mutations on the protein stability from its sequence. INPS is based on SVM regression and it is trained to predict the thermodynamic free energy change upon single-point variations in protein sequences. Results: We show that INPS performs similarly to the state-of-the-art methods based on protein structure when tested in cross-validation on a non-redundant dataset. INPS performs very well also on a newly generated dataset consisting of a number of variations occurring in the tumor suppressor protein p53. Our results suggest that INPS is a tool suited for computing the effect of non-synonymous polymorphisms on protein stability when the protein structure is not available. We also show that INPS predictions are complementary to those of the state-of-the-art, structure-based method mCSM. When the two methods are combined, the overall prediction on the p53 set scores significantly higher than those of the single methods.", "date": "2015-02-06T00:00:00Z", "citationCount": 111, "authors": [ { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw192", "pmid": "27153629", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "INPS-MD: A web server to predict stability of protein variants from sequence and structure", "abstract": "Motivation: Protein function depends on its structural stability. The effects of single point variations on protein stability can elucidate the molecular mechanisms of human diseases and help in developing new drugs. Recently, we introduced INPS, a method suited to predict the effect of variations on protein stability from protein sequence and whose performance is competitive with the available state-of-the-art tools. Results: In this article, we describe INPS-MD (Impact of Non synonymous variations on Protein Stability-Multi-Dimension), a web server for the prediction of protein stability changes upon single point variation from protein sequence and/or structure. Here, we complement INPS with a new predictor (INPS3D) that exploits features derived from protein 3D structure. INPS3D scores with Pearson's correlation to experimental ΔΔG values of 0.58 in cross validation and of 0.72 on a blind test set. The sequence-based INPS scores slightly lower than the structure-based INPS3D and both on the same blind test sets well compare with the state-of-the-art methods.", "date": "2016-08-15T00:00:00Z", "citationCount": 189, "authors": [ { "name": "Savojardo C." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "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": "Piero Fariselli", "email": "piero.fariselli@unito.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2016-05-04T15:36:53Z", "lastUpdate": "2025-03-17T14:54:19.762674Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA", "savo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "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. 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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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], "version": "1.1", "note": null, "metadata": { "title": "Bakta: Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification", "abstract": "Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command-line software pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates the precise assignment of public database cross-references. Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as well as comprehensive JSON files, facilitating automated downstream analysis. We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations, the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version is available at https://bakta.computational.bio.", "date": "2021-01-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Schwengers O." }, { "name": "Jelonek L." }, { "name": "Dieckmann M.A." }, { "name": "Beyvers S." }, { "name": "Blom J." }, { "name": "Goesmann A." } ], "journal": "Microbial Genomics" } } ], "credit": [ { "name": "Oliver Schwengers", "email": "oliver.schwengers@cb.jlug.de", "url": "https://github.com/oschwengers", "orcidid": "https://orcid.org/0000-0003-4216-2721", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Justus Liebig University Giessen", "email": null, "url": "https://www.uni-giessen.de", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "oschwengers", "additionDate": "2021-05-08T17:25:21Z", "lastUpdate": "2024-12-23T21:48:50.049892Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-CZ", "bebatut" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "TREND Protein Evolution Function", "description": "TREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. 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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. TREND is freely available at http://trend.zhulinlab.org.", "date": "2021-01-01T00:00:00Z", "citationCount": 33, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac034", "pmid": "35100406", "pmcid": "PMC8860576", "type": [ "Other" ], "version": null, "note": "Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937", "metadata": { "title": "Erratum: TREND: A platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)", "abstract": "TheURL address of the web server published in this article has been changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.", "date": "2022-02-22T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Gumerov V.M." }, { "name": "Zhulin I.B." } ], "journal": "Nucleic Acids Research" } } ], 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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. 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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 }, { "name": "UNRES server", "description": "A server implementation of the UNRES package for coarse-grained simulations of protein structures with the physics-based UNRES model. It can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. 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In contrast to most of the protein coarsegrained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user.", "date": "2018-07-02T00:00:00Z", "citationCount": 51, "authors": [ { "name": "Czaplewski C." }, { "name": "Karczynska A." }, { "name": "Sieradzan A.K." }, { "name": "Liwo A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Cezary Czaplewski", "email": "cezary.czaplewski@ug.edu.pl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Adam Liwo", "email": "adam.liwo@ug.edu.pl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-07-11T10:55:58Z", "lastUpdate": "2024-11-25T14:32:31.310937Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PDEStrIAn", "description": "The database revolves around the protein structure of catalytic PDE domains and the way PDE inhibitors can interact with them. 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The consistent structural alignment of 57 PDE ligand binding site residues enables the systematic analysis of PDE-ligand interaction fingerprints (IFPs), the identification of subtype-specific PDE-ligand interaction features, and the classification of ligands according to their binding modes. We illustrate how systematic mining of this phosphodiesterase structure and ligand interaction annotated (PDEStrIAn) database provides new insights into how conserved and selective PDE interaction hot spots can accommodate the large diversity of chemical scaffolds in PDE ligands. A substructure analysis of the cocrystallized PDE ligands in combination with those in the ChEMBL database provides a toolbox for scaffold hopping and ligand design. These analyses lead to an improved understanding of the structural requirements of PDE binding that will be useful in future drug discovery studies.", "date": "2016-08-11T00:00:00Z", "citationCount": 56, "authors": [ { "name": "Jansen C." }, { "name": "Kooistra A.J." }, { "name": "Kanev G.K." }, { "name": "Leurs R." }, { "name": "De Esch I.J.P." }, { "name": "De Graaf C." } ], "journal": "Journal of Medicinal Chemistry" } } ], "credit": [ { "name": "Division of Medicinal Chemistry (Vrije Universiteit Amsterdam)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Chris de Graaf", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Georgi K. 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User submitted sequences are automatically aligned and annotated according to their source organism and germline families.", "homepage": "http://www.biocomputing.it/proABC", "biotoolsID": "proabc", "biotoolsCURIE": "biotools:proabc", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2492", "term": "Protein interaction prediction" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0906", "term": "Protein interaction data" }, "format": [] } ], "note": "proABC estimates the residue-based probability for three different kind of interactions: Non-bonded Interactions, Hydrogen Bonds and Hydrophobic Interactions.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://circe.med.uniroma1.it/proABC/help_proABC.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt369", "pmid": "23803466", "pmcid": "PMC3753563", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Prediction of site-specific interactions in antibody-antigen complexes: The proABC method and server", "abstract": "Motivation: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. Results: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. © The Author 2013.", "date": "2013-09-15T00:00:00Z", "citationCount": 77, "authors": [ { "name": "Olimpieri P.P." }, { "name": "Chailyan A." }, { "name": "Tramontano A." }, { "name": "Marcatili P." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "ELIXIR-ITA-SAPIENZA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Pier Paolo Olimpieri", "email": "pierpaolo.olimpieri@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-SAPIENZA", "additionDate": "2015-01-22T11:49:01Z", "lastUpdate": "2024-11-25T14:26:05.307264Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "STITCH", "description": "Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.", "homepage": "http://stitch.embl.de/", "biotoolsID": "stitch", "biotoolsCURIE": "biotools:stitch", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" }, { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" }, { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_1199", "term": "InChIKey" }, { "uri": "http://edamontology.org/format_1196", "term": "SMILES" }, { "uri": "http://edamontology.org/format_3468", "term": "xls" } ] }, { "data": { "uri": "http://edamontology.org/data_1009", "term": "Protein name" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0990", "term": "Compound name" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "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_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_3547", "term": "Image format" } ] }, { "data": { "uri": "http://edamontology.org/data_0954", "term": "Database cross-mapping" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2042", "term": "Evidence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "STITCH is a database of protein – chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Its key function is to provide users with predictions about the interactions that their entities of interest (proteins or small molecules) may be making with other such entities, and to visualise where a set of entities of interest can be found within the STITCH network. Direct traceable links to the original sources on which interactions are described in the network, make it easy for users to trace the provenance of the data.", "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://stitch.embl.de/cgi/show_info_page.pl?UserId=pRfi11Qlkhnx&sessionId=sEfmbh_T7QLq", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkm795", "pmid": "18084021", "pmcid": "PMC2238848", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "STITCH: Interaction networks of chemicals and proteins", "abstract": "The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH ('search tool for interactions of chemicals') integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. STITCH is available at http://stitch.embl.de/. © 2007 The Author(s).", "date": "2008-01-01T00:00:00Z", "citationCount": 754, "authors": [ { "name": "Kuhn M." }, { "name": "von Mering C." }, { "name": "Campillos M." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkp937", "pmid": "19897548", "pmcid": "PMC2808890", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 2: An interaction network database for small molecules and proteins", "abstract": "Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74 000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-06T00:00:00Z", "citationCount": 231, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Franceschini A." }, { "name": "Campillos M." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Beyer A." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1207", "pmid": "24293645", "pmcid": "PMC3964996", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 4: Integration of protein-chemical interactions with user data", "abstract": "STITCH is a database of protein-chemical interactions that integrates many sources of experimental and manually curated evidence with text-mining information and interaction predictions. Available at http://stitch.embl.de, the resulting interaction network includes 390 000 chemicals and 3.6 million proteins from 1133 organisms. Compared with the previous version, the number of high-confidence protein-chemical interactions in human has increased by 45%, to 367 000. In this version, we added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data. For example, a user can now upload a spreadsheet with screening hits to easily check which interactions are already known. To increase the coverage of STITCH, we expanded the text mining to include full-text articles and added a prediction method based on chemical structures. We further changed our scheme for transferring interactions between species to rely on orthology rather than protein similarity. This improves the performance within protein families, where scores are now transferred only to orthologous proteins, but not to paralogous proteins. STITCH can be accessed with a web-interface, an API and downloadable files. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 413, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Pletscher-Frankild S." }, { "name": "Blicher T.H." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1011", "pmid": "22075997", "pmcid": "PMC3245073", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "STITCH 3: Zooming in on protein-chemical interactions", "abstract": "To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133 organisms. Compared to the previous version, the number of chemicals with interactions and the number of high-confidence interactions both increase 4-fold. The database can be accessed interactively through a web interface, displaying interactions in an integrated network view. It is also available for computational studies through downloadable files and an API. As an extension in the current version, we offer the option to switch between two levels of detail, namely whether stereoisomers of a given compound are shown as a merged entity or as separate entities. Separate display of stereoisomers is necessary, for example, for carbohydrates and chiral drugs. Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 250, "authors": [ { "name": "Kuhn M." }, { "name": "Szklarczyk D." }, { "name": "Franceschini A." }, { "name": "Von Mering C." }, { "name": "Jensen L.J." }, { "name": "Bork P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "EMBL", "email": null, "url": "http://www.embl.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "SUND-KU", "email": null, "url": "http://healthsciences.ku.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EC FP6", "email": null, "url": "http://ec.europa.eu/research/index.cfm", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "BMBF", "email": null, "url": "https://www.bmbf.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBO", "email": null, "url": "http://www.embo.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "CPR", "email": null, "url": "http://www.cpr.ku.dk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "TUD", "email": null, "url": "http://www.biotec.tu-dresden.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "HD-HuB", "email": null, "url": "https://www.hd-hub.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Michael Kuhn", "email": null, "url": "http://stitch1.embl.de/cgi/show_info_page.pl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null }, { "name": "Michael Kuhn", "email": null, "url": "http://stitch1.embl.de/cgi/show_info_page.pl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hdhub", "additionDate": "2016-02-17T09:43:56Z", "lastUpdate": "2024-11-25T14:25:13.779770Z", "editPermission": { "type": "group", "authors": [ "larsjuhljensen" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ModLink+", "description": "A tool predicts protein fold domain and family by means of sequence similarity and a relevant number of similar interactions (the same partners or is potential homologs).", "homepage": "http://sbi.imim.es/modlink/", "biotoolsID": "modlink", "biotoolsCURIE": "biotools:modlink", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1218", "term": "unambiguous pure protein" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://sbi.imim.es/modlink/modlinkhelp.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp238", "pmid": "19357100", "pmcid": "PMC2687990", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ModLink+: Improving fold recognition by using protein-protein interactions", "abstract": "Motivation: Several strategies have been developed to predict the fold of a target protein sequence, most of which are based on aligning the target sequence to other sequences of known structure. Previously, we demonstrated that the consideration of protein-protein interactions significantly increases the accuracy of fold assignment compared with PSI-BLAST sequence comparisons. A drawback of our method was the low number of proteins to which a fold could be assigned. Here, we present an improved version of the method that addresses this limitation. We also compare our method to other state-of-the-art fold assignment methodologies. Results: Our approach (ModLink+) has been tested on 3716 proteins with domain folds classified in the Structural Classification Of Proteins (SCOP) as well as known interacting partners in the Database of Interacting Proteins (DIP). For this test set, the ratio of success [positive predictive value (PPV)] on fold assignment increases from 75% for PSI-BLAST, 83% for HHSearch and 81% for PRC to >90% for ModLink+at the e-value cutoff of 10-3. Under this e-value, ModLink+can assign a fold to 30-45% of the proteins in the test set, while our previous method could cover <25%. When applied to 6384 proteins with unknown fold in the yeast proteome, ModLink+combined with PSI-BLAST assigns a fold for domains in 3738 proteins, while PSI-BLAST alone covers only 2122 proteins, HHSearch 2969 and PRC 2826 proteins, using a threshold e-value that would represent a PPV >82% for each method in the test set. © The Author 2009. Published by Oxford University Press. All rights reserved.", "date": "2009-06-09T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Fornes O." }, { "name": "Aragues R." }, { "name": "Espadaler J." }, { "name": "Marti-Renom M.A." }, { "name": "Sali A." }, { "name": "Oliva B." } ], "journal": "Bioinformatics" } }, { "doi": "10.1073/pnas.0500831102", "pmid": "15883372", "pmcid": "PMC1129109", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Detecting remotely related proteins by their interactions and sequence similarity", "abstract": "The function of an uncharacterized protein is usually inferred either from its homology to, or its interactions with, characterized proteins. Here, we use both sequence similarity and protein interactions to identify relationships between remotely related protein sequences. We rely on the fact that homologous sequences share similar interactions, and, therefore, the set of interacting partners of the partners of a given protein is enriched by its homologs. The approach was benchmarked by assigning the fold and functional family to test sequences of known structure. Specifically, we relied on 1,434 proteins with known folds, as defined in the Structural Classification of Proteins (SCOP) database, and with known interacting partners, as defined in the Database of Interacting Proteins (DIP). For this subset, the specificity of fold assignment was increased from 54% for position-specific iterative BLAST to 75% for our approach, with a concomitant increase in sensitivity for a few percentage points. Similarly, the specificity of family assignment at the e-value threshold of 10-8 was increased from 70% to 87%. The proposed method would be a useful tool for large-scale automated discovery of remote relationships between protein sequences, given its unique reliance on sequence similarity and protein-protein interactions. © 2005 by The National Academy of Sciences of the USA.", "date": "2005-05-17T00:00:00Z", "citationCount": 24, "authors": [ { "name": "Espadaler J." }, { "name": "Aragues R." }, { "name": "Eswar N." }, { "name": "Marti-Renom M.A." }, { "name": "Querol E." }, { "name": "Aviles F.X." }, { "name": "Sali A." }, { "name": "Oliva B." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } } ], "credit": [ { "name": "Jordi Espadaler", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-0128-8363", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Oriol Fornes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "upf.edu", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "baldo.oliva@upf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "baldo.oliva@upf.edu", "additionDate": "2016-04-22T12:06:06Z", "lastUpdate": "2024-11-25T14:24:59.636711Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SODA", "description": "Protein SOlubility based on Disorder and Aggregation", "homepage": "http://protein.bio.unipd.it/soda/", "biotoolsID": "soda-solubility", "biotoolsCURIE": "biotools:soda-solubility", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "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_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3538", "term": "Protein disordered structure" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "CC-BY-NC-ND-4.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://protein.bio.unipd.it/soda/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkx412", "pmid": "28505312", "pmcid": "PMC7059794", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "SODA: Prediction of protein solubility from disorder and aggregation propensity", "abstract": "Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility. It has been trained and benchmarked on two different datasets. The comparison to other recently published methods shows that SODA has state-of-the-art performance and is particularly well suited to predict mutations decreasing solubility. The method is fast, returning results for single mutations in seconds. A usage example estimating the full repertoire of mutations for a human germline antibody highlights several solubility hotspots on the surface.", "date": "2017-07-03T00:00:00Z", "citationCount": 47, "authors": [ { "name": "Paladin L." }, { "name": "Piovesan D." }, { "name": "Tosatto S.C.E." } ], "journal": "Nucleic Acids Research" } } ], "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": "http://orcid.org/0000-0003-4525-7793", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-PADOVA", "additionDate": "2018-03-12T09:31:50Z", "lastUpdate": "2024-11-25T14:23:38.672551Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }