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{ "count": 277, "next": "?page=2", "previous": null, "list": [ { "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": "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": "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. This server is free and there is no login requirement.", "date": "2023-07-05T00:00:00Z", "citationCount": 39, "authors": [ { "name": "Rey J." }, { "name": "Murail S." }, { "name": "De Vries S." }, { "name": "Derreumaux P." }, { "name": "Tuffery P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Julien Rey", "email": "julien.rey@u-paris.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-3050-511X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support", "Developer", "Primary contact" ], "note": null }, { "name": "Samuel Murail", "email": "samuel.muriail@u-paris.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-3842-5333", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Sjoerd de Vries", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-7701-3454", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Philippe Derreumaux", "email": "philippe.derreumaux@ibpc.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Pierre Tufféry", "email": "pierre.tuffery@inserm.fr", "url": null, "orcidid": "https://orcid.org/0000-0003-1033-9895", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "nchevrollier", "additionDate": "2025-03-04T16:25:28.372680Z", "lastUpdate": "2025-03-05T16:21:19.399517Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProteoMaker", "description": "ProteoMaker is a platform for the generation of an in-silico bottom-up proteomics data set with a ground truth on the level of proteoforms.", 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0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GPCRHMM", "description": "A hidden Markov model for GPCR detection.", "homepage": "http://gpcrhmm.sbc.su.se/", "biotoolsID": "gpcrhmm", "biotoolsCURIE": "biotools:gpcrhmm", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://gpcrhmm.sbc.su.se/instructions.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1110/ps.051745906", "pmid": "16452613", "pmcid": "PMC2249772", "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "bils.se", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.sbc.su.se/~erison/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mikael.borg@bils.se", "additionDate": "2015-12-07T13:03:43Z", "lastUpdate": "2024-11-25T14:55:26.899358Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HSYMDOCK", "description": "Symmetric protein docking for oligomers with Cn or Dn symmetry from the structure or sequence of a subunit molecule.", "homepage": "http://huanglab.phys.hust.edu.cn/hsymdock/", "biotoolsID": "hsymdock", "biotoolsCURIE": "biotools:hsymdock", "version": [ "2018-06-02" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" }, { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP" ], "license": 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 }, { "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. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run", "homepage": "http://unres-server.chem.ug.edu.pl/", "biotoolsID": "unres", "biotoolsCURIE": "biotools:unres", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "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_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0176", "term": "Molecular dynamics" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://unres-server.chem.ug.edu.pl/tutorial", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky328", "pmid": "29718313", "pmcid": "PMC6031057", "type": [], "version": null, "note": null, "metadata": { "title": "UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics", "abstract": "A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. 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": "proABC", "description": "Predictor of Antibody-Antigen interactions based on the Random Forest Algorithm. 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": "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 }, { "name": "RAVEN Toolbox", "description": "The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.", "homepage": "https://github.com/SysBioChalmers/RAVEN", "biotoolsID": "raven_toolbox", "biotoolsCURIE": "biotools:raven_toolbox", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_3660", "term": "Metabolic network modelling" }, { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1208", "term": "protein" } ] }, { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" }, { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] }, { "data": { "uri": "http://edamontology.org/data_3722", "term": "Physiology parameter" }, "format": [ { "uri": "http://edamontology.org/format_1957", "term": "raw" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3398", "term": "Bioengineering" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://gitter.im/SysBioChalmers/RAVEN", "type": [ "Mailing list" ], "note": "Gitter chat room" }, { "url": "https://github.com/SysBioChalmers/RAVEN/issues", "type": [ "Issue tracker" ], "note": "GitHub Issues" }, { "url": "https://github.com/SysBioChalmers/RAVEN", "type": [ "Repository" ], "note": "GitHub Repository" }, { "url": "https://github.com/SysBioChalmers/RAVEN/wiki", "type": [ "Helpdesk" ], "note": "GitHub Wiki" } ], "download": [ { "url": "https://github.com/SysBioChalmers/RAVEN/releases", "type": "Binaries", "note": "Stabile releases", "version": null }, { "url": "https://github.com/SysBioChalmers/RAVEN", "type": "Source code", "note": "Source code", "version": null } ], "documentation": [ { "url": "https://github.com/SysBioChalmers/RAVEN/wiki", "type": [ "General" ], "note": "GitHub Wiki" } ], "publication": [ { "doi": "10.1101/321067", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": null, "email": null, "url": "https://gitter.im/SysBioChalmers/RAVEN?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Hao Wang", "email": "hao.wang@chalmers.se", "url": null, "orcidid": "http://orcid.org/0000-0001-7475-0136", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "eduardk", "additionDate": "2018-07-18T09:31:39Z", "lastUpdate": "2024-11-25T14:23:23.622737Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PIGS", "description": "Web server for the automatic modeling of immunoglobulin variable domains based on the canonical structure method. It has a user-friendly and flexible interface, that allows the user to choose templates (for the frameworks and the loops) and modeling strategies in an automatic or manual fashion.", "homepage": "http://circe.med.uniroma1.it/pigs/", "biotoolsID": "pigs", "biotoolsCURIE": "biotools:pigs", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "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_1460", "term": "Protein structure" }, "format": [] } ], "note": "Automatic prediction of immunoglobulin structures.", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "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/pigs/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nprot.2014.189", "pmid": "25375991", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Antibody structural modeling with prediction of immunoglobulin structure (PIGS)", "abstract": "Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (~10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.", "date": "2014-11-20T00:00:00Z", "citationCount": 54, "authors": [ { "name": "Marcatili P." }, { "name": "Olimpieri P.P." }, { "name": "Chailyan A." }, { "name": "Tramontano A." } ], "journal": "Nature Protocols" } }, { "doi": "10.1093/bioinformatics/btn341", "pmid": "18641403", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "PIGS: Automatic prediction of antibody structures", "abstract": "We describe a web server for the automatic prediction of immunoglobulin variable domains based on the canonical structure model. The server is user-friendly and flexible. It allows the user to select the templates for the frameworks and the loops using different strategies. The final output is a full-fledged 3D model of the variable domains of the target immunoglobulin. © The Author 2008. Published by Oxford University Press. All rights reserved.", "date": "2008-09-01T00:00:00Z", "citationCount": 153, "authors": [ { "name": "Marcatili P." }, { "name": "Rosi A." }, { "name": "Tramontano A." } ], "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": "Paolo Marcatili", "email": "paolo.marcatili@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-SAPIENZA", "additionDate": "2015-01-22T11:49:04Z", "lastUpdate": "2024-11-25T14:21:19.179245Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SIB-BLAST", "description": "SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.", "homepage": "http://bioserv.mps.ohio-state.edu/sib-blast/", "biotoolsID": "sib-blast", "biotoolsCURIE": "biotools:sib-blast", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3315", "term": "Mathematics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST utility" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://bioserv.mps.ohio-state.edu/sib-blast/Manual.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkp301", "pmid": "19429693", "pmcid": "PMC2703926", "type": [], "version": null, "note": null, "metadata": { "title": "SIB-BLAST: A web server for improved delineation of true and false positives in PSI-BLAST searches", "abstract": "A SIB-BLAST web server (http://sib-blast.osc.edu) has been established for investigators to use the SimpleIsBeautiful (SIB) algorithm for sequence-based homology detection. SIB was developed to overcome the model corruption frequently observed in the later iterations of PSI-BLAST searches. The algorithm compares resultant hits from the second iteration to the final iteration of a PSI-BLAST search, calculates the figure of merit for each 'overlapped' hit and re-ranks the hits according to their figure of merit. By validating hits generated from the last profile against hits from the first profile when the model is least corrupted, the true and false positives are better delineated, which in turn, improves the accuracy of iterative PSI-BLAST searches. Notably, this improvement to PSI-BLAST comes at minimal computational cost as SIB-BLAST utilizes existing results already produced in a PSI-BLAST search.", "date": "2009-08-04T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Lee M.M." }, { "name": "Chan M.K." }, { "name": "Bundschuh R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ralf Bundschuh", "email": "bundschuh@mps.ohio-state.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-24T14:34:16Z", "lastUpdate": "2024-11-25T14:18:19.816961Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AUTOHD", "description": "Analysis of H/D-exchange data using isotopic distributions.", "homepage": "http://www.ms-utils.org/autohd.html", "biotoolsID": "autohd", "biotoolsCURIE": "biotools:autohd", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0404", "term": "Protein hydrogen exchange rate calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2200", "term": "FASTA-like (text)" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1537", "term": "Protein structure report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/autohd_download.html", "type": "Source code", "note": null, "version": null }, { "url": "http://www.ms-utils.org/autohd_download.html", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.ms-utils.org/autohd.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/s1044-0305(01)00301-4", "pmid": "11720389", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions", "abstract": "High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P. Copyright © 2001 American Society for Mass Spectrometry.", "date": "2001-12-01T00:00:00Z", "citationCount": 62, "authors": [ { "name": "Palmblad M." }, { "name": "Buijs J." }, { "name": "Hakansson P." } ], "journal": "Journal of the American Society for Mass Spectrometry" } } ], "credit": [ { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:45Z", "lastUpdate": "2024-11-25T14:16:56.803274Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioLCCC", "description": "An analytic model of peptide retention.", "homepage": "http://theorchromo.ru/", "biotoolsID": "biolccc", "biotoolsCURIE": "biotools:biolccc", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3633", "term": "Retention time prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2979", "term": "Peptide property" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://packages.python.org/pyteomics.biolccc/API/mespaceBioLCCC.html", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://theorchromo.ru/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ac060913x", "pmid": "17105170", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Liquid chromatography at critical conditions: Comprehensive approach to sequence-dependent retention time prediction", "abstract": "An approach to sequence-dependent retention time prediction of peptides based on the concept of liquid chromatography at critical conditions (LCCC) is presented. Within the LCCC approach applied to biopolymers (BioLCCC), the specific retention time corresponds to a particular sequence. In combination with mass spectrometry, this approach provides an efficient tool to solve problems wherein the protein sequencing is essential. In this work, we present a theoretical background of the BioLCCC concept and demonstrate experimentally its feasibility for sequence-dependent LC retention time prediction for peptides. BioLCCC model is based on three notions: (a) a random walk model for a macromolecule chain; (b) an entropy and energy compensation for the macromolecules within the adsorbent pore; and (c) a set of phenomenological parameters for the effective interaction energies of interactions between the amino acid residues and the adsorbent surface. In this work, the phenomenological parameters have been obtained for C18 reversed-phase HPLC. Note, that contrary to alternative additive models for retention time prediction based on summation of the so-called \"retention coefficients\", the BioLCCC approach takes into account the location of amino acids within the primary structure of a peptide and, thus, allows the identification of the peptides having the same composition of amino acids but differing by their arrangement. As a result, this new approach allows prediction of retention time for any possible amino acid sequence in particular HPLC experiments. In addition, the BioLCCC model lacks of main drawbacks of additive approaches that predict retention time for sequences of limited chain lengths and provide information about amino acid composition only. The proposed BioLCCC approach was characterized experimentally using LTQ FT LC-MS and LC-MS/MS data obtained earlier for Escherichia coli. The HPLC system calibration was performed using peptide retention standards. The results received show a linear correlation between predicted and experimental retention times, with a correlation coefficient, R2, of 0.97 for a peptide standard mixture and 0.9 for E. coli data, respectively, with the standard error below 1 min. The work presents the first description of a BioLCCC approach for high-throughput peptide characterization and preliminary results of its feasibility tests. © 2006 American Chemical Society.", "date": "2006-11-15T00:00:00Z", "citationCount": 71, "authors": [ { "name": "Gorshkov A.V." }, { "name": "Tarasova I.A." }, { "name": "Evreinov V.V." }, { "name": "Savitski M.M." }, { "name": "Nielsen M.L." }, { "name": "Zubarev R.A." }, { "name": "Gorshkov M.V." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:51:06Z", "lastUpdate": "2024-11-25T14:16:48.686997Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "decoy.pl", "description": "Decoy database generator from Matrix Science.", "homepage": "http://www.matrixscience.com/help/decoy_help.html", "biotoolsID": "decoy.pl", "biotoolsCURIE": "biotools:decoy.pl", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0364", "term": "Random sequence generation" } ], "input": [ { "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_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2546", "term": "FASTA-like" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.matrixscience.com/downloads/decoy.pl.gz", "type": "Source code", "note": null, "version": null }, { "url": "http://www.matrixscience.com/downloads/decoy.pl.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.matrixscience.com/help/decoy_help.html#MANUAL", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth785", "pmid": "16118637", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations", "abstract": "Researchers have several options when designing proteomics experiments. Primary among these are choices of experimental method, instrumentation and spectral interpretation software. To evaluate these choices on a proteome scale, we compared triplicate measurements of the yeast proteome by liquid chromatography tandem mass spectrometry (LC-MS/MS) using linear ion trap (LTQ) and hybrid quadrupole time-of-flight (QqTOF; QSTAR) mass spectrometers. Acquired MS/MS spectra were interpreted with Mascot and SEQUEST algorithms with and without the requirement that all returned peptides be tryptic. Using a composite target decoy database strategy, we selected scoring criteria yielding 1% estimated false positive identifications at maximum sensitivity for all data sets, allowing reasonable comparisons between them. These comparisons indicate that Mascot and SEQUEST yield similar results for LTQ-acquired spectra but less so for QSTAR spectra. Furthermore, low reproducibility between replicate data acquisitions made on one or both instrument platforms can be exploited to increase sensitivity and confidence in large-scale protein identifications.", "date": "2005-09-01T00:00:00Z", "citationCount": 620, "authors": [ { "name": "Elias J.E." }, { "name": "Haas W." }, { "name": "Faherty B.K." }, { "name": "Gygi S.P." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "msutils_import", "additionDate": "2017-01-17T14:52:01Z", "lastUpdate": "2024-11-25T14:16:09.448059Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "massXpert", "description": "Tool for analysis of polymer and peptide/protein mass spectra.", "homepage": "http://www.massxpert.org", "biotoolsID": "massxpert", "biotoolsCURIE": "biotools:massxpert", "version": [ "massXpert 2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0365", "term": "Nucleic acid restriction digest" }, { "uri": "http://edamontology.org/operation_0417", "term": "Post-translation modification site prediction" }, { "uri": "http://edamontology.org/operation_0564", "term": "Sequence visualisation" }, { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_0239", "term": "Sequence motif recognition" }, { "uri": "http://edamontology.org/operation_3023", "term": "Prediction and recognition (protein)" }, { "uri": "http://edamontology.org/operation_3024", "term": "Prediction and recognition (nucleic acid)" }, { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0977", "term": "Tool identifier" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0977", "term": "Tool identifier" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3292", "term": "Biochemistry" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3511", "term": "Nucleic acid sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://download.tuxfamily.org/massxpert/source/", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1093/bioinformatics/btp504", "pmid": "19740912", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "massXpert 2: A cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data", "abstract": "Since the middle of the 90s, mass spectrometry has evolved into an almost indispensable tool in structural studies on an ever-growing variety of (bio-)polymers, of which proteins, sugars and nucleic acids are the most prominent. Since the first public release of massXpert, the advances of mass spectrometry have motivated continuous and thorough maintenance of that software, in the form of two full software rewrites, culminating with massXpert 2, which we describe in this report. We shall describe the profound changes in massXpert that were performed so as to keep up with the technical advances in mass spectrometry since a decade. © The Author 2009. Published by Oxford University Press. All rights reserved.", "date": "2009-10-20T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Rusconi F." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "massXpert", "email": "massxpert-maintainer@massxpert.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "rusconi", "additionDate": "2017-01-17T14:50:36Z", "lastUpdate": "2024-11-25T14:09:16.386925Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Protter", "description": "Interactive protein feature visualization and integration with experimental proteomic data.", "homepage": "http://wlab.ethz.ch/protter/", "biotoolsID": "protter", "biotoolsCURIE": "biotools:protter", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2241", "term": "Transmembrane protein visualisation" }, { "uri": "http://edamontology.org/operation_2486", "term": "Topology diagram drawing" }, { "uri": "http://edamontology.org/operation_0472", "term": "GPCR prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_3636", "term": "MRM/SRM" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_2547", "term": "uniprotkb-like format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [ { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_2547", "term": "uniprotkb-like format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] }, { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" }, { "uri": "http://edamontology.org/format_2547", "term": "uniprotkb-like format" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1709", "term": "Protein secondary structure image" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0128", "term": "Protein interactions" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://ulo.github.io/Protter/", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://wlab.ethz.ch/protter/help/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt607", "pmid": "24162465", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protter: Interactive protein feature visualization and integration with experimental proteomic data", "abstract": "Summary: The ability to integrate and visualize experimental proteomic evidence in the context of rich protein feature annotations represents an unmet need of the proteomics community. Here we present Protter, a web-based tool that supports interactive protein data analysis and hypothesis generation by visualizing both annotated sequence features and experimental proteomic data in the context of protein topology. Protter supports numerous proteomic file formats and automatically integrates a variety of reference protein annotation sources, which can be readily extended via modular plug-ins. A built-in export function produces publication-quality customized protein illustrations, also for large datasets. Visualizations of surfaceome datasets show the specific utility of Protter for the integrated visual analysis of membrane proteins and peptide selection for targeted proteomics. © 2013 The Author 2013. Published by Oxford University Press. All rights reserved.", "date": "2014-03-01T00:00:00Z", "citationCount": 948, "authors": [ { "name": "Omasits U." }, { "name": "Ahrens C.H." }, { "name": "Muller S." }, { "name": "Wollscheid B." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Ulrich Omasits", "email": "protter@imsb.biol.ethz.ch", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null }, { "name": null, "email": "webmaster@ms-utils.org", "url": "http://ms-utils.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Documentor" ], "note": null } ], "owner": "ulo", "additionDate": "2017-01-17T14:50:42Z", "lastUpdate": "2024-11-25T14:08:43.785732Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MEROPS Blast", "description": "Search MEROPS sequences with BLAST.", "homepage": "http://merops.sanger.ac.uk/cgi-bin/blast/submitblast/merops/advanced", "biotoolsID": "merops_blast", "biotoolsCURIE": "biotools:merops_blast", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3494", "term": "DNA sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0857", "term": "Sequence search results" }, "format": [] } ], "note": "The output includes protein similarity matches with active site residues annotated", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "http://merops.sanger.ac.uk/about/special_features.shtml#BLAST", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1118", "pmid": "26527717", "pmcid": "PMC4702814", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors", "abstract": "The MEROPS database (http://merops.sanger.ac.UK) is an integrated source of information about peptidases, their substrates and inhibitors, which are of great relevance to biology, medicine and biotechnology. The hierarchical classification of the database is as follows: homologous sets of sequences are grouped into a protein species; protein species are grouped into a family; families are grouped into clans. There is a type example for each protein species (known as a 'holotype'), family and clan, and each protein species, family and clan has its own unique identifier. Pages to show the involvement of peptidases and peptidase inhibitors in biological pathways have been created. Each page shows the peptidases and peptidase inhibitors involved in the pathway, along with the known substrate cleavages and peptidase-inhibitor interactions, and a link to the KEGG database of biological pathways. Links have also been established with the IUPHAR Guide to Pharmacology. A new service has been set up to allow the submission of identified substrate cleavages so that conservation of the cleavage site can be assessed. This should help establish whether or not a cleavage site is physiologically relevant on the basis that such a cleavage site is likely to be conserved.", "date": "2016-01-01T00:00:00Z", "citationCount": 558, "authors": [ { "name": "Rawlings N.D." }, { "name": "Barrett A.J." }, { "name": "Finn R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Neil Rawlings", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "MEROPS group", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "NCBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Sanger Institute", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "merops@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "MEROPS group", "email": "merops@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:47:47Z", "lastUpdate": "2024-11-25T14:07:28.092820Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Kinase SARfari BLAST Search", "description": "BLAST search against Kinase domains stored in Kinase SARfari.", "homepage": "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/protein", "biotoolsID": "kinase_sarfari_blast_search", "biotoolsCURIE": "biotools:kinase_sarfari_blast_search", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "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_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST", "ChEMBL Tools", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/chembl/sarfari/kinasesarfari/protein", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr777", "pmid": "21948594", "pmcid": "PMC3245175", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ChEMBL: A large-scale bioactivity database for drug discovery", "abstract": "ChEMBL is an Open Data database containing binding, functional and ADMET information for a large number of drug-like bioactive compounds. These data are manually abstracted from the primary published literature on a regular basis, then further curated and standardized to maximize their quality and utility across a wide range of chemical biology and drug-discovery research problems. Currently, the database contains 5.4 million bioactivity measurements for more than 1 million compounds and 5200 protein targets. Access is available through a web-based interface, data downloads and web services at: https://www.ebi.ac.uk/ chembldb. © The Author(s) 2011. Published by Oxford University Press.", "date": "2012-01-01T00:00:00Z", "citationCount": 3079, "authors": [ { "name": "Gaulton A." }, { "name": "Bellis L.J." }, { "name": "Bento A.P." }, { "name": "Chambers J." }, { "name": "Davies M." }, { "name": "Hersey A." }, { "name": "Light Y." }, { "name": "McGlinchey S." }, { "name": "Michalovich D." }, { "name": "Al-Lazikani B." }, { "name": "Overington J.P." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "ChEMBL Team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "chembl-help@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Mark Davies", "email": "mdavies@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:44:10Z", "lastUpdate": "2024-11-25T14:07:26.688810Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Malaria Data BLAST Search", "description": "BLAST search against protein targets stored in Malaria Data database.", "homepage": "https://www.ebi.ac.uk/chembl/malaria/target", "biotoolsID": "malaria_data_blast_search", "biotoolsCURIE": "biotools:malaria_data_blast_search", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "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_0857", "term": "Sequence search results" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST", "ChEMBL Tools", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/chembl/malaria/target", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkr777", "pmid": "21948594", "pmcid": "PMC3245175", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ChEMBL: A large-scale bioactivity database for drug discovery", "abstract": "ChEMBL is an Open Data database containing binding, functional and ADMET information for a large number of drug-like bioactive compounds. These data are manually abstracted from the primary published literature on a regular basis, then further curated and standardized to maximize their quality and utility across a wide range of chemical biology and drug-discovery research problems. Currently, the database contains 5.4 million bioactivity measurements for more than 1 million compounds and 5200 protein targets. Access is available through a web-based interface, data downloads and web services at: https://www.ebi.ac.uk/ chembldb. © The Author(s) 2011. 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It does so by integrating a number of publicly available data sources, which have subsequently been used to build data mining services, predictive tools and visualizations for drug metabolism researchers. The data include the interactions of small molecules with ADME (absorption, distribution, metabolism and excretion) proteins responsible for the metabolism and transport of molecules; available pharmacokinetic (PK) data; protein sequences of ADME-related molecular targets for pre-clinical model species and human; alignments of the orthologues including information on known SNPs (Single Nucleotide Polymorphism) and information on the tissue distribution of these proteins. 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In response, the services and infrastructure of the European Bioinformatics Institute (EMBL-EBI, www.ebi.ac.UK) are continually expanding: total disk capacity increases significantly every year to keep pace with demand (75 petabytes as of December 2015), and interoperability between resources remains a strategic priority. Since 2014 we have launched two new resources: the European Variation Archive for genetic variation data and EMPIAR for two-dimensional electron microscopy data, as well as a Resource Description Framework platform. We also launched the Embassy Cloud service, which allows users to run large analyses in a virtual environment next to EMBL-EBI's vast public data resources.", "date": "2016-01-01T00:00:00Z", "citationCount": 98, "authors": [ { "name": "Cook C.E." }, { "name": "Bergman M.T." }, { "name": "Finn R.D." }, { "name": "Cochrane G." }, { "name": "Birney E." }, { "name": "Apweiler R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "ChEMBL Team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "chembl-help@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Mark Davies", "email": "mdavies@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:44:11Z", "lastUpdate": "2024-11-25T14:07:19.272422Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ChEMBL BLAST Search", "description": "BLAST search against protein targets stored in ChEMBL database.", "homepage": "https://www.ebi.ac.uk/chembl/target", "biotoolsID": "chembl_blast_search", "biotoolsCURIE": "biotools:chembl_blast_search", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "blast", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" } ], "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_0962", "term": "Small molecule report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_2258", "term": "Cheminformatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "BLAST", "ChEMBL Tools", "ChEMBL", "EBI Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/chembl/target", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkw1074", "pmid": "27899562", "pmcid": "PMC5210557", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The ChEMBL database in 2017", "abstract": "ChEMBL is an open large-scale bioactivity database (https://www.ebi.ac.uk/chembl), previously described in the 2012 and 2014 Nucleic Acids Research Database Issues. Since then, alongside the continued extraction of data from the medicinal chemistry literature, new sources of bioactivity data have also been added to the database. These include: deposited data sets from neglected disease screening; crop protection data; drug metabolism and disposition data and bioactivity data from patents. A number of improvements and new features have also been incorporated. These include the annotation of assays and targets using ontologies, the inclusion of targets and indications for clinical candidates, addition of metabolic pathways for drugs and calculation of structural alerts. The ChEMBL data can be accessed via a web-interface, RDF distribution, data downloads and RESTful web-services.", "date": "2017-01-01T00:00:00Z", "citationCount": 1665, "authors": [ { "name": "Gaulton A." }, { "name": "Hersey A." }, { "name": "Nowotka M.-L." }, { "name": "Patricia Bento A." }, { "name": "Chambers J." }, { "name": "Mendez D." }, { "name": "Mutowo P." }, { "name": "Atkinson F." }, { "name": "Bellis L.J." }, { "name": "Cibrian-Uhalte E." }, { "name": "Davies M." }, { "name": "Dedman N." }, { "name": "Karlsson A." }, { "name": "Magarinos M.P." }, { "name": "Overington J.P." }, { "name": "Papadatos G." }, { "name": "Smit I." }, { "name": "Leach A.R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "ChEMBL Team", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "chembl-help@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Mark Davies", "email": "mdavies@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "EMBL-EBI", "additionDate": "2015-01-29T15:44:15Z", "lastUpdate": "2024-11-25T14:07:14.708062Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }