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{ "count": 2303, "next": "?page=2", "previous": null, "list": [ { "name": "PIA - Protein Inference Algorithms", "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.", "homepage": "https://github.com/medbioinf/pia", "biotoolsID": "pia", "biotoolsCURIE": "biotools:pia", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "knime", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3713", "term": "Mascot .dat file" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3684", "term": "PRIDE XML" }, { "uri": "http://edamontology.org/format_3711", "term": "X!Tandem XML" }, { "uri": "http://edamontology.org/format_3702", "term": "MSF" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] } ], "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "BioInfra.Prot", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/medbioinf/pia", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/pia", "type": "Source code", "note": null, "version": null }, { "url": "http://bioconda.github.io/recipes/pia/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/mpc-bioinformatics/pia/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://hub.docker.com/r/julianusz/pia", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/medbioinf/pia/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.5b00121", "pmid": "25938255", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface", "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.", "date": "2015-07-02T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Uszkoreit J." }, { "name": "Maerkens A." }, { "name": "Perez-Riverol Y." }, { "name": "Meyer H.E." }, { "name": "Marcus K." }, { "name": "Stephan C." }, { "name": "Kohlbacher O." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.8b00723", "pmid": "30474983", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats", "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.", "date": "2019-02-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Uszkoreit J." }, { "name": "Perez-Riverol Y." }, { "name": "Eggers B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": "julian.uszkoreit@rub.de", "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "CUBiMed.RUB", "email": "cubimed@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "julianu", "additionDate": "2016-07-12T10:54:05Z", "lastUpdate": "2025-05-02T13:15:26.717477Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenMS", "description": "Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. 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"term": "Annotation" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" }, { "uri": "http://edamontology.org/operation_3705", "term": "Isotope-coded protein label" }, { "uri": "http://edamontology.org/operation_3634", "term": "Label-free quantification" }, { "uri": "http://edamontology.org/operation_3639", "term": "iTRAQ" }, { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3694", "term": "Mass spectrum visualisation" }, { "uri": "http://edamontology.org/operation_3635", "term": "Labeled quantification" }, { "uri": "http://edamontology.org/operation_3359", "term": "Splitting" }, { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3649", 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"http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3683", "term": "qcML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Workbench" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C++" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "OpenMS" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OpenMS/OpenMS", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/OpenMS/OpenMS", "type": "Source code", "note": null, "version": null }, { "url": "http://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/", "type": "Binaries", "note": null, "version": null }, { "url": "https://github.com/OpenMS/OpenMS", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/nmeth.3959", "pmid": "27575624", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "OpenMS: A flexible open-source software platform for mass spectrometry data analysis", "abstract": "© 2016 Nature America, Inc. All rights reserved.High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing cellular signaling networks. However, the rapid growth in the volume and complexity of MS data makes transparent, accurate and reproducible analysis difficult. We present OpenMS 2.0 (http://www.openms.de), a robust, open-source, cross-platform software specifically designed for the flexible and reproducible analysis of high-throughput MS data. The extensible OpenMS software implements common mass spectrometric data processing tasks through a well-defined application programming interface in C++ and Python and through standardized open data formats. OpenMS additionally provides a set of 185 tools and ready-made workflows for common mass spectrometric data processing tasks, which enable users to perform complex quantitative mass spectrometric analyses with ease.", "date": "2016-08-30T00:00:00Z", "citationCount": 246, "authors": [ { "name": "Rost H.L." }, { "name": "Sachsenberg T." }, { "name": "Aiche S." }, { "name": "Bielow C." }, { "name": "Weisser H." }, { "name": "Aicheler F." }, { "name": "Andreotti S." }, { "name": "Ehrlich H.-C." }, { "name": "Gutenbrunner P." }, { "name": "Kenar E." }, { "name": "Liang X." }, { "name": "Nahnsen S." }, { "name": "Nilse L." }, { "name": "Pfeuffer J." }, { "name": "Rosenberger G." }, { "name": "Rurik M." }, { "name": "Schmitt U." }, { "name": "Veit J." }, { "name": "Walzer M." }, { "name": "Wojnar D." }, { "name": "Wolski W.E." }, { "name": "Schilling O." }, { "name": "Choudhary J.S." }, { "name": "Malmstrom L." }, { "name": "Aebersold R." }, { "name": "Reinert K." }, { "name": "Kohlbacher O." } ], "journal": "Nature Methods" } }, { "doi": "10.1007/978-1-60761-987-1_23", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "OpenMS and TOPP: open source software for LC-MS data analysis.", "abstract": "Proteomics experiments based on state-of-the-art mass spectrometry produce vast amounts of data, which cannot be analyzed manually. Hence, software is needed which is able to analyze the data in an automated fashion. The need for robust and reusable software tools triggered the development of libraries implementing different algorithms for the various analysis steps. OpenMS is such a software library and provides a wealth of data structures and algorithms for the analysis of mass spectrometric data. For users unfamiliar with programming, TOPP (\"The OpenMS Proteomics Pipeline\") offers a wide range of already implemented tools sharing the same interface and designed for a specific analysis task each. TOPP thus makes the sophisticated algorithms of OpenMS accessible to nonprogrammers. The individual TOPP tools can be strung together into pipelines for analyzing mass spectrometry-based experiments starting from the raw output of the mass spectrometer. These analysis pipelines can be constructed using a graphical editor. Even complex analytical workflows can thus be analyzed with ease.", "date": "2011-01-01T00:00:00Z", "citationCount": 65, "authors": [ { "name": "Bertsch A." }, { "name": "Gropl C." }, { "name": "Reinert K." }, { "name": "Kohlbacher O." } ], "journal": "Methods in molecular biology (Clifton, N.J.)" } } ], "credit": [ { "name": "ETH Zürich", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Eberhard-Karls-Universität Tübingen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Freie Universität Berlin", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Center for Integrative Bioinformatics (CiBi)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null }, { "name": "cibi", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "General Mailinglist", "email": "open-ms-general@lists.sourceforge.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Support" ], "note": null }, { "name": "General Mailinglist", "email": "open-ms-general@lists.sourceforge.net", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Hannes Röst", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-0990-7488", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "samwein", "additionDate": "2016-01-19T16:39:56Z", "lastUpdate": "2025-04-30T11:39:30.251890Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pyOpenMS", "description": "Python library for mass spectrometry, specifically for the analysis of proteomics and metabolomics data.", "homepage": "https://github.com/OpenMS/pyopenms-extra/blob/master/docs/source/index.rst", "biotoolsID": "pyOpenMS", "biotoolsCURIE": "biotools:pyOpenMS", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "BSD-3-Clause", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/OpenMS/pyopenms-extra", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/OpenMS/pyopenms-extra/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [ { "url": "https://pyopenms.readthedocs.io", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.7287/PEERJ.PREPRINTS.27736", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Hannes L. Rost", "email": "hannes.rost@utoronto.ca", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "samwein", "additionDate": "2019-08-09T13:16:33Z", "lastUpdate": "2025-04-30T11:39:29.549782Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenSWATH", "description": "OpenSWATH is a proteomics software that allows analysis of LC-MS/MS DIA (data independent acquisition) and implemented as part of OpenMS.", "homepage": "http://www.openswath.org", "biotoolsID": "OpenSWATH", "biotoolsCURIE": "biotools:OpenSWATH", "version": [ "OpenMS 2.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental 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spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" }, { "uri": "http://edamontology.org/format_3621", "term": "SQLite format" }, { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] }, { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3246", "term": "TraML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3833", "term": "featureXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3621", "term": "SQLite format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": 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"https://buildmedia.readthedocs.org/media/pdf/openswath/latest/openswath.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": null, "pmid": "24727770", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data", "abstract": "", "date": "2014-01-01T00:00:00Z", "citationCount": 409, "authors": [ { "name": "Rost H.L." }, { "name": "Rosenberger G." }, { "name": "Navarro P." }, { "name": "Gillet L." }, { "name": "Miladinovia S.M." }, { "name": "Schubert O.T." }, { "name": "Wolski W." }, { "name": "Collins B.C." }, { "name": "Malmstrom J." }, { "name": "Malmstrom L." }, { "name": "Aebersold R." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": "Hannes Röst", "email": "hroest@stanford.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "George Rosenberger", "email": "gr2578@cumc.columbia.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "samwein", "additionDate": "2019-06-18T11:06:01Z", "lastUpdate": "2025-04-30T11:39:29.102190Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OpenPepXL", "description": "An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS.\n\nProtein-Protein Cross-Linking (OpenPepXL) – OpenMS.\n\nOpenPepXL is a protein-protein cross-link identification tool implemented in C++ as part of OpenMS. It works with all uncleavable labeled and label-free cross-linkers but not (yet) with cleavable ones.", "homepage": "https://openms.org/openpepxl", "biotoolsID": "openpepxl", "biotoolsCURIE": "biotools:openpepxl", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": "BSD-3-Clause", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.openms.de/openpepxl", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/MCP.TIR120.002186", "pmid": "33067342", "pmcid": "PMC7710140", "type": [], "version": null, "note": null, "metadata": { "title": "OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS", "abstract": "© 2020 Netz et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc.Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared with other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Because of efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of noncleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a data set from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenPepXL finds from 7% to over 50% more unique residue pairs (URPs) than other tools. On data sets with available high-resolution structures for cross-link validation OpenPepXL reports from 7% to over 40% more structurally validated URPs than other tools. Additionally, we used a synthetic peptide data set that allows objective validation of cross-links without relying on structural information and found that OpenPepXL reports at least 12% more validated URPs than other tools. It has been built as part of the OpenMS suite of tools and supports Windows, macOS, and Linux operating systems. OpenPepXL also supports the MzIdentML 1.2 format for XL-MS identification results. It is freely available under a three-clause BSD license at https://openms.org/openpepxl.", "date": "2020-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Netz E." }, { "name": "Dijkstra T.M.H." }, { "name": "Sachsenberg T." }, { "name": "Zimmermann L." }, { "name": "Walzer M." }, { "name": "Monecke T." }, { "name": "Ficner R." }, { "name": "Dybkov O." }, { "name": "Urlaub H." }, { "name": "Kohlbacher O." } ], "journal": "Molecular and Cellular Proteomics" } } ], "credit": [ { "name": "Eugen Netz", "email": "eugen.netz@tuebingen.mpg.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Oliver Kohlbacher", "email": "oliver.kohlbacher@uni-tuebingen.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "samwein", "additionDate": "2021-01-18T11:10:26Z", "lastUpdate": "2025-04-30T11:39:28.349250Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "compareMS2", "description": "compareMS2 is a tool for comparing sets of (tandem) mass spectra for clustering samples, molecular phylogenetics, identification of biological species or tissues, and quality control. compareMS2 currently consumes Mascot Generic Format, or MGF, and produces output in a variety of common image and distance matrix formats.", "homepage": "https://github.com/524D/compareMS2", "biotoolsID": "comparems2", "biotoolsCURIE": "biotools:comparems2", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2424", "term": "Comparison" }, { "uri": "http://edamontology.org/operation_0567", "term": "Phylogenetic tree visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3272", "term": "Species tree" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" }, { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_2855", "term": "Distance matrix" }, "format": [ { "uri": "http://edamontology.org/format_1991", "term": "mega" }, { "uri": "http://edamontology.org/format_1912", "term": "Nexus format" }, { "uri": "http://edamontology.org/format_1910", "term": "newick" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0084", "term": "Phylogeny" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C", "JavaScript" ], "license": "MIT", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/524D/compareMS2", "type": [ "Repository" ], "note": null }, { "url": "https://www.ms-utils.org/compareMS2.html", "type": [ "Software catalogue" ], "note": null }, { "url": "https://research-software-directory.org/software/comparems2", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.html", "type": "Binaries", "note": null, "version": "1.0" }, { "url": "http://www.ms-utils.org/compareMS2.c", "type": "Source code", "note": null, "version": "1.0" }, { "url": "https://github.com/524D/compareMS2/tree/main/src", "type": "Source code", "note": null, "version": "2.0" }, { "url": "https://github.com/524D/compareMS2/tree/main", "type": "Binaries", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://www.ms-utils.org/compareMS2.html", "type": [ "General", "Command-line options" ], "note": null }, { "url": "https://github.com/524D/compareMS2", "type": [ "General", "User manual", "Command-line options", "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.6162", "pmid": "22368051", "pmcid": null, "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "Molecular phylogenetics by direct comparison of tandem mass spectra", "abstract": "Rationale: Molecular phylogenetics is the study of evolution and relatedness of organisms or genes. Mass spectrometry is used routinely for bacterial identification and has also been used for phylogenetic analysis, for instance from bone material. Unfortunately, only a small fraction of the acquired tandem mass spectra allow direct interpretation. Methods: We describe a new algorithm and software for molecular phylogenetics using pairwise comparisons of tandem mass spectra from enzymatically digested proteins. The spectra need not be annotated and all acquired data is used in the analysis. To demonstrate the method, we analyzed tryptic digests of sera from four great apes and two other primates. Results: The distribution of spectra dot products for thousands of tandem mass spectra collected from two samples provides a measure on the fraction of shared peptides between the two samples. When inverted, this becomes a distance metric. By pairwise comparison between species and averaging over four individuals per species, it was possible to reconstruct the unique correct phylogenetic tree for the great apes and other primates. Conclusions: The new method described here has several attractive features compared with existing methods, among them simplicity, the unbiased use of all acquired data rather than a small subset of spectra, and the potential use of heavily degraded proteins or proteins with a priori unknown modifications. © 2012 John Wiley & Sons, Ltd.", "date": "2012-04-15T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Palmblad M." }, { "name": "Deelder A.M." } ], "journal": "Rapid Communications in Mass Spectrometry" } }, { "doi": "10.1021/acs.jproteome.2c00457", "pmid": "36173614", "pmcid": "PMC9903320", "type": [ "Primary" ], "version": "2.0", "note": null, "metadata": { "title": "compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets", "abstract": "It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.", "date": "2023-02-03T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Marissen R." }, { "name": "Varunjikar M.S." }, { "name": "Laros J.F.J." }, { "name": "Rasinger J.D." }, { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.1c00528", "pmid": "34523928", "pmcid": "PMC8491155", "type": [ "Review" ], "version": "2.0", "note": null, "metadata": { "title": "Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics", "abstract": "Science is full of overlooked and undervalued research waiting to be rediscovered. Proteomics is no exception. In this perspective, we follow the ripples from a 1960 study of Zuckerkandl, Jones, and Pauling comparing tryptic peptides across animal species. This pioneering work directly led to the molecular clock hypothesis and the ensuing explosion in molecular phylogenetics. In the decades following, proteins continued to provide essential clues on evolutionary history. While technology has continued to improve, contemporary proteomics has strayed from this larger biological context, rarely comparing species or asking how protein structure, function, and interactions have evolved. Here we recombine proteomics with molecular phylogenetics, highlighting the value of framing proteomic results in a larger biological context and how almost forgotten research, though technologically surpassed, can still generate new ideas and illuminate our work from a different perspective. Though it is infeasible to read all research published on a large topic, looking up older papers can be surprisingly rewarding when rediscovering a \"gem\"at the end of a long citation chain, aided by digital collections and perpetually helpful librarians. Proper literature study reduces unnecessary repetition and allows research to be more insightful and impactful by truly standing on the shoulders of giants. All data was uploaded to MassIVE (https://massive.ucsd.edu/) as dataset MSV000087993.", "date": "2021-10-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Neely B.A." }, { "name": "Palmblad M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "lumc.nl", "email": null, "url": "https://www.lumc.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Support" ], "note": null }, { "name": "Magnus Palmblad", "email": "magnus.palmblad@gmail.com", "url": "https://github.com/magnuspalmblad", "orcidid": "http://orcid.org/0000-0002-5865-8994", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact", "Documentor" ], "note": null }, { "name": "Rob Marissen", "email": null, "url": "https://github.com/524D", "orcidid": "https://orcid.org/0000-0002-1220-9173", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "n.m.palmblad@lumc.nl", "additionDate": "2016-04-15T11:52:42Z", "lastUpdate": "2025-04-16T14:22:04.957317Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "neXtProt", "description": "neXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.", "homepage": "https://www.expasy.org/archives/nextprot", "biotoolsID": "nextprot", "biotoolsCURIE": "biotools:nextprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "Rare Disease", "Proteomics" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/calipho-sib/", "type": [ "Repository" ], "note": "neXtProt software repository with issue tracking" }, { "url": "https://twitter.com/nextprot_news", "type": [ "Social media" ], "note": "neXtProt release news, publications, presentations, tips and more. DM us with feedback!" }, { "url": "https://www.expasy.org/resources/nextprot", "type": [ "Software catalogue" ], "note": "neXtProt entry in Expasy" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkz995", "pmid": "31724716", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The neXtProt knowledgebase in 2020: Data, tools and usability improvements", "abstract": "The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.", "date": "2020-01-01T00:00:00Z", "citationCount": 155, "authors": [ { "name": "Zahn-Zabal M." }, { "name": "Michel P.-A." }, { "name": "Gateau A." }, { "name": "Nikitin F." }, { "name": "Schaeffer M." }, { "name": "Audot E." }, { "name": "Gaudet P." }, { "name": "Duek P.D." }, { "name": "Teixeira D." }, { "name": "De Laval V.R." }, { "name": "Samarasinghe K." }, { "name": "Bairoch A." }, { "name": "Lane L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1179", "pmid": "22139911", "pmcid": "PMC3245017", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NeXtProt: A knowledge platform for human proteins", "abstract": "neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Lane L." }, { "name": "Argoud-Puy G." }, { "name": "Britan A." }, { "name": "Cusin I." }, { "name": "Duek P.D." }, { "name": "Evalet O." }, { "name": "Gateau A." }, { "name": "Gaudet P." }, { "name": "Gleizes A." }, { "name": "Masselot A." }, { "name": "Zwahlen C." }, { "name": "Bairoch A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Support", "email": "support@nextprot.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pascale Gaudet", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-1813-6857", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "SIB", "additionDate": "2015-01-21T13:30:06Z", "lastUpdate": "2025-04-02T08:05:19.163091Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "mzahn", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WeSA", "description": "WeSA, (weighted socioaffinity), is a statistical score which can rank results from protein experiments of the bait-prey type, e.g. affinity purification, immunoprecipitation or proximity labelling.\n\nYou can enter lists of interacting proteins according to the results of your experiment. Input your raw data before any filtering is done.\n\nAs a result you will get a re-ordered list of scores which allows one to understand which interactions are more likely than others based on what previous experiments can add to your data.", "homepage": "https://wesa.russelllab.org/", "biotoolsID": "we_sa", "biotoolsCURIE": "biotools:we_sa", "version": [], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3957", "term": "Protein interaction experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": null, "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/russelllab/wesa", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://wesa.russelllab.org/help", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae423", "pmid": "38795065", "pmcid": "PMC11223876", "type": [], "version": null, "note": null, "metadata": { "title": "WeSA: A web server for improving analysis of affinity proteomics data", "abstract": "Protein-protein interaction experiments still yield many false positive interactions. The socioaffinity metric can distinguish true protein-protein interactions from noise based on available data. Here, we present WeSA (Weighted SocioAffinity), which considers large datasets of interaction proteomics data (IntAct, BioGRID, the BioPlex) to score human protein interactions and, in a statistically robust way, flag those (even from a single experiment) that are likely to be false positives. ROC analysis (using CORUM-PDB positives and Negatome negatives) shows that WeSA improves over other measures of interaction confidence. WeSA shows consistently good results over all datasets (up to: AUC = 0.93 and at best threshold: TPR = 0.84, FPR = 0.11, Precision = 0.98). WeSA is freely available without login (wesa.russelllab.org). Users can submit their own data or look for organized information on human protein interactions using the web server. Users can either retrieve available information for a list of proteins of interest or calculate scores for new experiments. The server outputs either pre-computed or updated WeSA scores for the input enriched with information from databases. The summary is presented as a table and a network-based visualization allowing the user to remove those nodes/edges that the method considers spurious.", "date": "2024-07-05T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Shtetinska M.M." }, { "name": "Gonzalez-Sanchez J.-C." }, { "name": "Beyer T." }, { "name": "Boldt K." }, { "name": "Ueffing M." }, { "name": "Russell R.B." } ], "journal": "Nucleic Acids Research" } } ], "credit": [], "owner": "Pub2Tools", "additionDate": "2025-03-28T11:13:12.813456Z", "lastUpdate": "2025-03-28T12:14:32.901305Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "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": "MetIDfyR", "description": "Open-Source R Package to Decipher Small-Molecule Drugs Metabolism Through High Resolution Mass Spectrometry.\n\nMetIDfyR is an open-source, cross-platform and versatile R script to predict and detect metabolites in mass spectrometry data (mzML) based on the raw formula of the drug of interest.", "homepage": "https://github.com/agnesbrnb/MetIDfyR", "biotoolsID": "metidfyr", "biotoolsCURIE": "biotools:metidfyr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] }, { "data": { "uri": "http://edamontology.org/data_0846", "term": "Chemical formula" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Script" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3375", "term": "Drug metabolism" }, { "uri": "http://edamontology.org/topic_3370", "term": "Analytical chemistry" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/agnesbrnb/MetIDfyR", "type": [ "Quick start guide", "Installation instructions", "Citation instructions" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.analchem.0c02281", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "MetIDfyR: An Open-Source R Package to Decipher Small-Molecule Drug Metabolism through High-Resolution Mass Spectrometry", "abstract": "With recent advances in analytical chemistry, liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential tool for metabolite discovery and detection. Even if most of the common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, complicating metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited. In this article, we present MetIDfyR, an open-source and cross-platform R package for in silico drug phase I/II biotransformation prediction and mass-spectrometric data mining. MetIDfyR has proven its efficacy for advanced metabolite identification in semi-complex and complex mixtures in in vitro or in vivo drug studies and is freely available at github.com/agnesblch/MetIDfyR.", "date": "2020-10-06T00:00:00Z", "citationCount": 10, "authors": [ { "name": "Delcourt V." }, { "name": "Barnabe A." }, { "name": "Loup B." }, { "name": "Garcia P." }, { "name": "Andre F." }, { "name": "Chabot B." }, { "name": "Trevisiol S." }, { "name": "Moulard Y." }, { "name": "Popot M.-A." }, { "name": "Bailly-Chouriberry L." } ], "journal": "Analytical Chemistry" } } ], "credit": [], "owner": "agnesbarnabe", "additionDate": "2021-01-18T09:08:27Z", "lastUpdate": "2025-02-27T15:46:01.807140Z", "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.", "homepage": "https://github.com/computproteomics/ProteoMaker", "biotoolsID": "proteomaker", "biotoolsCURIE": "biotools:proteomaker", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3566", "term": "Simulated gene expression data generation" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "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_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1238", "term": "Proteolytic digest" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [ { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] }, { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3524", "term": "Simulation experiment" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R" ], "license": "MIT", "collectionID": [ "Proteomics" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://computproteomics.bmb.sdu.dk/app_direct/ProteoMaker", "type": [ "Service" ], "note": "Web application" } ], "download": [ { "url": "https://github.com/computproteomics/ProteoMaker", "type": "Source code", "note": null, "version": null } ], "documentation": [], "publication": [], "credit": [], "owner": "veitveit11", "additionDate": "2025-01-31T17:19:47.094256Z", "lastUpdate": "2025-01-31T17:19:47.096981Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MetaboMAPS", "description": "Pathway sharing and multi-omics data visualization in metabolic context.\n\nMetaboMAPS is a web project for manipulating metabolic pathways in SVG format. MetaboMAPS consists of two main parts: the visualization tool, where users can plot their own data set, and the plot box editor, where users can add or change the areas for visualization (plot boxes) and assign identifiers to them.", "homepage": "https://metabomaps.brenda-enzymes.org", "biotoolsID": "metabomaps", "biotoolsCURIE": "biotools:metabomaps", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_3929", "term": "Metabolic pathway prediction" }, { "uri": "http://edamontology.org/operation_3926", "term": "Pathway visualisation" }, { "uri": "http://edamontology.org/operation_2943", "term": "Box-Whisker plot plotting" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Library", "Web application" ], "topic": [ { 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"term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Repository" ], "note": null }, { "url": "http://phistruct.bioinfodlsu.com/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/bioinfodlsu/PHIStruct", "type": [ "Installation instructions", "Quick start guide", "Citation instructions", "Command-line 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In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.", "homepage": "https://cran.r-project.org/package=MALDIquant", "biotoolsID": "maldi_quant", "biotoolsCURIE": "biotools:maldi_quant", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3799", "term": "Quantification" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2048", "term": "Report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [ { "uri": "http://edamontology.org/format_3603", "term": "PNG" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2536", "term": "Mass spectrometry data" }, "format": [ { "uri": "http://edamontology.org/format_3682", "term": "imzML metadata file" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sgibb/MALDIquant/", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/sgibb/MALDIquant/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "http://strimmerlab.org/software/maldiquant/", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://cran.r-project.org/web/packages/MALDIquant/MALDIquant.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts447", "pmid": "22796955", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Maldiquant: A versatile R package for the analysis of mass spectrometry data", "abstract": "MALDIquant is an R package providing a complete and modular analysis pipeline for quantitative analysis of mass spectrometry data. MALDIquant is specifically designed with application in clinical diagnostics in mind and implements sophisticated routines for importing raw data, preprocessing, non-linear peak alignment and calibration. It also handles technical replicates as well as spectra with unequal resolution. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-09-01T00:00:00Z", "citationCount": 476, "authors": [ { "name": "Gibb S." }, { "name": "Strimmer K." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Sebastian Gibb", "email": "mail@sebastiangibb.de", "url": null, "orcidid": "https://orcid.org/0000-0001-7406-4443", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "Korbinian Strimmer", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-7917-2056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "owner": "Kigaard", "additionDate": "2021-05-26T20:42:18Z", "lastUpdate": "2024-12-15T19:31:00.871136Z", "editPermission": { "type": "group", "authors": [ "sizhengZhao" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ESIprot", "description": "Charge state determination and molecular weight calculation for low resolution electrospray ionization data.", "homepage": "https://nube-gran.de/esiprot", "biotoolsID": "esiprot", "biotoolsCURIE": "biotools:esiprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0398", "term": "Protein molecular weight calculation" }, { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3629", "term": "Deisotoping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0944", "term": "Peptide mass fingerprint" }, "format": [ { "uri": "http://edamontology.org/format_3245", "term": "Mass spectrometry data format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": "GPL-3.0", "collectionID": [ "ms-utils", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.bioprocess.org/esiprot/esiprot_form.php", "type": [ "Mirror" ], "note": null }, { "url": "http://ms-utils.org", "type": [ "Software catalogue" ], "note": null } ], "download": [ { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null }, { "url": "http://www.bioprocess.org/esiprot/esiprot.zip", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/rcm.4384", "pmid": "20049890", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "ESIprot: A universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data", "abstract": "Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2Da, the relative errors below 30ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software. © 2010 John Wiley & Sons, Ltd.", "date": "2010-01-01T00:00:00Z", "citationCount": 75, "authors": [ { "name": "Winkler R." } ], "journal": "Rapid Communications in Mass Spectrometry" } } ], "credit": [ { "name": "Robert Winkler", "email": "robert.winkler@ira.cinvestav.mx", "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": "2017-01-17T14:50:59Z", "lastUpdate": "2024-12-13T13:53:01.317118Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PolySTest", "description": "Robust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.", "homepage": "http://computproteomics.bmb.sdu.dk/Apps/PolySTest", "biotoolsID": "PolySTest", "biotoolsCURIE": "biotools:PolySTest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3664", "term": "Statistical modelling" }, { "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_3751", "term": "DSV" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3932", "term": "Q-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_3905", "term": "Histogram" }, "format": [ { "uri": "http://edamontology.org/format_3604", "term": "SVG" } ] }, { "data": { "uri": "http://edamontology.org/data_0928", "term": "Gene expression profile" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "GPL-2.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bitbucket.org/veitveit/polystest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1074/mcp.RA119.001777", "pmid": "32424025", "pmcid": "PMC8015005", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "owner": "veits@bmb.sdu.dk", "additionDate": "2019-11-14T19:27:27Z", "lastUpdate": "2024-11-25T16:09:23.465736Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "2D-PAGE", "description": "2D-PAGE database.", "homepage": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi", "biotoolsID": "2d-page", "biotoolsCURIE": "biotools:2d-page", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2373", "term": "Spot ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2091", "term": "Accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1519", "term": "Peptide molecular weights" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1528", "term": "Protein isoelectric point" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0897", "term": "Protein property" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] }, { "data": { "uri": "http://edamontology.org/data_0942", "term": "2D PAGE image" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1528", "term": "Protein isoelectric point" }, "format": [] } ], "note": "This is the main interface of the Make2D-DB II tool to query SIENA 2D-DATABASE. Search by accession number or entry name (AC or ID),\nby description, or UniProtKB/Swiss-Prot keywords. General information, 2D-gel spot location and picture of gel.", "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "DRCAT", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.200300483", "pmid": "12923769", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Make 2D-DB II package: Conversion of federated two-dimensional gel electrophoresis databases into a relational format and interconnection of distributed databases", "abstract": "The Make 2D-DB tool has been previously developed to help build federated two-dimensional gel electrophoresis (2-DE) databases on one's own web site. The purpose of our work is to extend the strength of the first package and to build a more efficient environment. Such an environment should be able to fulfill the different needs and requirements arising from both the growing use of 2-DE techniques and the increasing amount of distributed experimental data.", "date": "2003-08-01T00:00:00Z", "citationCount": 27, "authors": [ { "name": "Mostaguir K." }, { "name": "Hoogland C." }, { "name": "Binz P.-A." }, { "name": "Appel R.D." } ], "journal": "Proteomics" } } ], "credit": [ { "name": "University of Siena, Italy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "DRCAT", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": "Luca Bini", "email": "bini@unisi.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "DRCAT", "additionDate": "2015-09-11T17:01:36Z", "lastUpdate": "2024-11-25T14:17:26.650772Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3dLOGO", "description": "3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.", "homepage": "http://3dlogo.uniroma2.it/3dLOGO/home.html", "biotoolsID": "3dlogo", "biotoolsCURIE": "biotools:3dlogo", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0448", "term": "Sequence alignment analysis (conservation)" }, { "uri": "http://edamontology.org/operation_0245", "term": "Protein structural motif recognition" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkm228", "pmid": "17488847", "pmcid": "PMC1933223", "type": [], "version": null, "note": null, "metadata": { "title": "3dLOGO: A web server for the identification, analysis and use of conserved protein substructures", "abstract": "3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/. © 2007 The Author(s).", "date": "2007-07-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Via A." }, { "name": "Peluso D." }, { "name": "Gherardini P.F." }, { "name": "De Rinaldis E." }, { "name": "Colombo T." }, { "name": "Ausiello G." }, { "name": "Helmer-Citterich M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1006/jmbi.1998.2248", "pmid": "9837739", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Three-dimensional profiles: A new tool to identify protein surface similarities", "abstract": "We report a procedure for the description and comparison of protein surfaces, which is based on a three-dimensional (3D) transposition of the profile method for sensitive protein homology sequence searches. Although the principle of the method can be applied to detect similarities to a single protein surface, the possibility of extending this approach to protein families displaying common structural and/or functional properties, makes it a more powerful tool. In analogy to profiles derived from the multiple alignment of protein sequences, we derive a 3D surface profile from a protein structure or from a multiple structure alignment of several proteins. The 3D profile is used to screen the protein structure database, searching for similar protein surfaces. The application of the procedure to SH2 and SH3 binding pockets and to the nucleotide binding pocket associated with the p-loop structural motif is described. The SH2 and SH3 3D profiles can identify all the SH2 and SH3 binding regions present in the test dataset; the p-loop 3D profile is able to recognize all the p-loop-containing proteins present in the test dataset. Analysis of the p-loop 3D profile allowed the identification of a positive charge whose position is conserved in space but not in sequence. The best ranking non-p-loop-containing protein is an ADP-forming succinyl coenzyme A synthetase, whose nucleotide-binding region has not yet been identified.", "date": "1998-12-11T00:00:00Z", "citationCount": 42, "authors": [ { "name": "De Rinaldis M." }, { "name": "Ausiello G." }, { "name": "Cesareni G." }, { "name": "Helmer-Citterich M." } ], "journal": "Journal of Molecular Biology" } }, { "doi": "10.1186/1471-2105-5-50", "pmid": "15119965", "pmcid": "PMC420233", "type": [], "version": null, "note": null, "metadata": { "title": "A structural study for the optimisation of functional motifs encoded in protein sequences", "abstract": "Background. A large number of PROSITE patterns select false positives and/or miss known true positives. It is possible that - at least in some cases - the weak specificity and/or sensitivity of a pattern is due to the fact that one, or maybe more, functional and/or structural key residues are not represented in the pattern. Multiple sequence alignments are commonly used to build functional sequence patterns. If residues structurally conserved in proteins sharing a function cannot be aligned in a multiple sequence alignment, they are likely to be missed in a standard pattern construction procedure. Results. Here we present a new procedure aimed at improving the sensitivity and/ or specificity of poorly-performing patterns. The procedure can be summarised as follows: 1. residues structurally conserved in different proteins, that are true positives for a pattern, are identified by means of a computational technique and by visual inspection. 2. the sequence positions of the structurally conserved residues falling outside the pattern are used to build extended sequence patterns. 3. the extended patterns are optimised on the SWISS-PROT database for their sensitivity and specificity. The method was applied to eight PROSITE patterns. Whenever structurally conserved residues are found in the surface region close to the pattern (seven out of eight cases), the addition of information inferred from structural analysis is shown to improve pattern selectivity and in some cases selectivity and sensitivity as well. In some of the cases considered the procedure allowed the identification of functionally interesting residues, whose biological role is also discussed. Conclusion. Our method can be applied to any type of functional motif or pattern (not only PROSITE ones) which is not able to select all and only the true positive hits and for which at least two true positive structures are available. The computational technique for the identification of structurally conserved residues is already available on request and will be soon accessible on our web server. The procedure is intended for the use of pattern database curators and of scientists interested in a specific protein family for which no specific or selective patterns are yet available. © 2004 Via and Helmer-Citterich, licensee BioMed Central Ltd.", "date": "2004-04-30T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Via A." }, { "name": "Helmer-Citterich M." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1186/1471-2105-6-s4-s5", "pmid": "16351754", "pmcid": "PMC1866380", "type": [], "version": null, "note": null, "metadata": { "title": "Query3d: A new method for high-throughput analysis of functional residues in protien structures", "abstract": "Background: The identification of local similarities between two protein structures can provide clues of a common function. Many different methods exist for searching for similar subsets of residues in proteins of known structure. However, the lack of functional and structural information on single residues, together with the low level of integration of this information in comparison methods, is a limitation that prevents these methods from being fully exploited in high-throughput analyses. Results: Here we describe Query3d, a program that is both a structural DBMS (Database Management System) and a local comparison method. The method conserves a copy of all the residues of the Protein Data Bank annotated with a variety of functional and structural information. New annotations can be easily added from a variety of methods and known databases. The algorithm makes it possible to create complex queries based on the residues' function and then to compare only subsets of the selected residues. Functional information is also essential to speed up the comparison and the analysis of the results. Conclusion: With Query3d, users can easily obtain statistics on how many and which residues share certain properties in all proteins of known structure. At the same time, the method also finds their structural neighbours in the whole PDB. Programs and data can be accessed through the PdbFun web interface.", "date": "2005-12-01T00:00:00Z", "citationCount": 50, "authors": [ { "name": "Ausiello G." }, { "name": "Via A." }, { "name": "Helmer-Citterich M." } ], "journal": "BMC Bioinformatics" } } ], "credit": [], "owner": "ELIXIR-EE", "additionDate": "2017-02-14T09:34:42Z", "lastUpdate": "2024-11-25T14:17:22.357136Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "3Omics", "description": "A web based systems biology visualization tool for integrating human transcriptomic, proteomic and metabolomic data.", "homepage": "https://3omics.cmdm.tw/", "biotoolsID": "3omics", "biotoolsCURIE": "biotools:3omics", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://3omics.cmdm.tw/help.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1752-0509-7-64", "pmid": "23875761", "pmcid": "PMC3723580", "type": [], "version": null, "note": null, "metadata": { "title": "3Omics: A web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data", "abstract": "Background: Integrative and comparative analyses of multiple transcriptomics, proteomics and metabolomics datasets require an intensive knowledge of tools and background concepts. Thus, it is challenging for users to perform such analyses, highlighting the need for a single tool for such purposes. The 3Omics one-click web tool was developed to visualize and rapidly integrate multiple human inter- or intra-transcriptomic, proteomic, and metabolomic data by combining five commonly used analyses: correlation networking, coexpression, phenotyping, pathway enrichment, and GO (Gene Ontology) enrichment.Results: 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for all transcripts, proteins and metabolites. If only two of three omics datasets are input, then 3Omics supplements the missing transcript, protein or metabolite information related to the input data by text-mining the PubMed database. 3Omics' coexpression analysis assists in revealing functions shared among different omics datasets. 3Omics' phenotype analysis integrates Online Mendelian Inheritance in Man with available transcript or protein data. Pathway enrichment analysis on metabolomics data by 3Omics reveals enriched pathways in the KEGG/HumanCyc database. 3Omics performs statistical Gene Ontology-based functional enrichment analyses to display significantly overrepresented GO terms in transcriptomic experiments. Although the principal application of 3Omics is the integration of multiple omics datasets, it is also capable of analyzing individual omics datasets. The information obtained from the analyses of 3Omics in Case Studies 1 and 2 are also in accordance with comprehensive findings in the literature.Conclusions: 3Omics incorporates the advantages and functionality of existing software into a single platform, thereby simplifying data analysis and enabling the user to perform a one-click integrated analysis. Visualization and analysis results are downloadable for further user customization and analysis. The 3Omics software can be freely accessed at http://3omics.cmdm.tw. © 2013 Kuo et al.; licensee BioMed Central Ltd.", "date": "2013-07-13T00:00:00Z", "citationCount": 148, "authors": [ { "name": "Kuo T.-C." }, { "name": "Tian T.-F." }, { "name": "Tseng Y.J." } ], "journal": "BMC Systems Biology" } } ], "credit": [ { "name": "Yufeng Jane Tseng", "email": "yjtseng@csie.ntu.edu.tw", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-17T19:04:18Z", "lastUpdate": "2024-11-25T14:17:20.979256Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ADEPTS", "description": "Software package for peptide identification using two different types of MS/MS spectra.", "homepage": "https://cs.uwaterloo.ca/~l22he/", "biotoolsID": "adepts", "biotoolsCURIE": "biotools:adepts", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/adepts-advanced-peptide-de-novo-sequencing-with-a-pair-of-tandem-mass-spectra.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1142/s0219720010005099", "pmid": "21121022", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Adepts: Advanced peptide de novo sequencing with a pair of tandem mass spectra", "abstract": "De novo sequencing is an important task in proteomics to identify novel peptide sequences. Traditionally, only one MS/MS spectrum is used for the sequencing of a peptide; however, the use of multiple spectra of the same peptide with different types of fragmentation has the potential to significantly increase the accuracy and practicality of de novo sequencing. Research into the use of multiple spectra is in a nascent stage. We propose a general framework to combine the two different types of MS/MS data. Experiments demonstrate that our method significantly improves the de novo sequencing of existing software. © 2010 Imperial College Press.", "date": "2010-12-01T00:00:00Z", "citationCount": 29, "authors": [ { "name": "He L." }, { "name": "Ma B." } ], "journal": "Journal of Bioinformatics and Computational Biology" } } ], "credit": [ { "name": null, "email": null, "url": "https://cs.uwaterloo.ca/~l22he/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:34Z", "lastUpdate": "2024-11-25T14:17:19.618187Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ALL-P", "description": "Statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. It performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect.", "homepage": "http://pappso.inra.fr/bioinfo/all_p/index.php", "biotoolsID": "all-p", "biotoolsCURIE": "biotools:all-p", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3321", "term": "Molecular genetics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/all-p-including-shared-peptides-estimating-protein-abundances.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://pappso.inra.fr/bioinfo/all_p/download.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/pmic.201100660", "pmid": "22833229", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Including shared peptides for estimating protein abundances: A significant improvement for quantitative proteomics", "abstract": "Inferring protein abundances from peptide intensities is the key step in quantitative proteomics. The inference is necessarily more accurate when many peptides are taken into account for a given protein. Yet, the information brought by the peptides shared by different proteins is commonly discarded. We propose a statistical framework based on a hierarchical modeling to include that information. Our methodology, based on a simultaneous analysis of all the quantified peptides, handles the biological and technical errors as well as the peptide effect. In addition, we propose a practical implementation suitable for analyzing large data sets. Compared to a method based on the analysis of one protein at a time (that does not include shared peptides), our methodology proved to be far more reliable for estimating protein abundances and testing abundance changes. The source codes are available at http://pappso.inra.fr/bioinfo/all_p/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.", "date": "2012-09-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Blein-Nicolas M." }, { "name": "Xu H." }, { "name": "de Vienne D." }, { "name": "Giraud C." }, { "name": "Huet S." }, { "name": "Zivy M." } ], "journal": "Proteomics" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.inra.fr/les_recherches/annuaires/autres/microbiologie/pappso_plate_forme_d_analyses_proteomiques_de_paris_sud_ouest", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:41Z", "lastUpdate": "2024-11-25T14:17:18.441827Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AMYLPRED", "description": "Consensus prediction method for identifying possible amyloidogenic regions in protein sequences.", "homepage": "http://aias.biol.uoa.gr/AMYLPRED/", "biotoolsID": "amylpred", "biotoolsCURIE": "biotools:amylpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_0417", "term": "Protein post-translation modification site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/amylpred-a-consensus-method-for-amyloid-propensity-prediction.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://aias.biol.uoa.gr/AMYLPRED/login.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1472-6807-9-44", "pmid": "19589171", "pmcid": "PMC2714319", "type": [], "version": null, "note": null, "metadata": { "title": "Amyloidogenic determinants are usually not buried", "abstract": "Background. Amyloidoses are a group of usually fatal diseases, probably caused by protein misfolding and subsequent aggregation into amyloid fibrillar deposits. The mechanisms involved in amyloid fibril formation are largely unknown and are the subject of current, intensive research. In an attempt to identify possible amyloidogenic regions in proteins for further experimental investigation, we have developed and present here a publicly available online tool that utilizes five different and independently published methods, to form a consensus prediction of amyloidogenic regions in proteins, using only protein primary structure data. Results. It appears that the consensus prediction tool is slightly more objective than individual prediction methods alone and suggests several previously not identified amino acid stretches as potential amyloidogenic determinants, which (although several of them may be overpredictions) require further experimental studies. The tool is available at: http://biophysics.biol.uoa.gr/AMYLPRED. Utilizing molecular graphics programs, like O and PyMOL, as well as the algorithm DSSP, it was found that nearly all experimentally verified amyloidogenic determinants (short peptide stretches favouring aggregation and subsequent amyloid formation), and several predicted, with the aid of the tool AMYLPRED, but not experimentally verified amyloidogenic determinants, are located on the surface of the relevant amyloidogenic proteins. This finding may be important in efforts directed towards inhibiting amyloid fibril formation. Conclusion. The most significant result of this work is the observation that virtually all, to date, experimentally determined amyloidogenic determinants and the majority of predicted, but not yet experimentally verified short amyloidogenic stretches, lie 'exposed' on the surface of the relevant amyloidogenic proteins, and also several of them have the ability to act as conformational 'switches'. Experiments, focused on these fragments, should be performed to test this idea. © 2009 Frousios et al; licensee BioMed Central Ltd.", "date": "2009-07-30T00:00:00Z", "citationCount": 128, "authors": [ { "name": "Frousios K.K." }, { "name": "Iconomidou V.A." }, { "name": "Karletidi C.-M." }, { "name": "Hamodrakas S.J." } ], "journal": "BMC Structural Biology" } } ], "credit": [ { "name": null, "email": "shamodr@biol.uoa.gr", "url": "http://biophysics.biol.uoa.gr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:47Z", "lastUpdate": "2024-11-25T14:17:16.586759Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANARCI", "description": "Tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains.", "homepage": "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php", "biotoolsID": "anarci", "biotoolsCURIE": "biotools:anarci", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/anarci-antigen-receptor-numbering-and-receptor-classification.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv552", "pmid": "26424857", "pmcid": "PMC4708101", "type": [], "version": null, "note": null, "metadata": { "title": "ANARCI: Antigen receptor numbering and receptor classification", "abstract": "Motivation: Antibody amino-acid sequences can be numbered to identify equivalent positions. Such annotations are valuable for antibody sequence comparison, protein structure modelling and engineering. Multiple different numbering schemes exist, they vary in the nomenclature they use to annotate residue positions, their definitions of position equivalence and their popularity within different scientific disciplines. However, currently no publicly available software exists that can apply all the most widely used schemes or for which an executable can be obtained under an open license. Results: ANARCI is a tool to classify and number antibody and T-cell receptor amino-acid variable domain sequences. It can annotate sequences with the five most popular numbering schemes: Kabat, Chothia, Enhanced Chothia, IMGT and AHo. Availability and implementation: ANARCI is available for download under GPLv3 license at opig.stats.ox.ac.uk/webapps/anarci. A web-interface to the program is available at the same address. Contact:", "date": "2016-01-15T00:00:00Z", "citationCount": 193, "authors": [ { "name": "Dunbar J." }, { "name": "Deane C.M." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://opig.stats.ox.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:48Z", "lastUpdate": "2024-11-25T14:17:15.343704Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AnDom", "description": "Web tool that helps to assign structural domains to protein sequences and to classify them according to SCOP.", "homepage": "http://andom.bioapps.biozentrum.uni-wuerzburg.de/index_new.html", "biotoolsID": "andom", "biotoolsCURIE": "biotools:andom", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2996", "term": "Structure classification" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/andom-assign-structual-domains-protein-sequences.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://andom.bioapps.biozentrum.uni-wuerzburg.de/Usage_new.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ci010374r", "pmid": "11911710", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A versatile structural domain analysis server using profile weight matrices", "abstract": "The WEB tool \"AnDom\" assigns to a given protein sequence all experimentally determined structural domains contained within it, including multidomain and large proteins. The server uses profile specific matrices from custom generated multiple sequence alignments of all known SCOP domains (SCOP version 1.50). Prediction time is short allowing numerous applications for structural genomics including investigation of complex eucaryotic protein families. The WWW server is at http://www.bork.embl-heidelberg.de/AnDom, and profiles can be downloaded at ftp.bork.embl-heidelberg.de/pub/users/schmidt/AnDom.", "date": "2002-03-01T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Schmidt S." }, { "name": "Bork P." }, { "name": "Dandekar T." } ], "journal": "Journal of Chemical Information and Computer Sciences" } } ], "credit": [ { "name": "Dominik Schaack & Steffen Schmidt", "email": null, "url": "http://www.bork.embl.de/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:20Z", "lastUpdate": "2024-11-25T14:17:13.978877Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANM", "description": "Simple NMA tool for analysis of vibrational motions in molecular systems. It uses Elastic Network (EN) methodology and represents the system in the residue level.", "homepage": "http://anm.csb.pitt.edu/", "biotoolsID": "anm", "biotoolsCURIE": "biotools:anm", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_2476", "term": "Molecular dynamics simulation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB", "Perl", "C" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/anm-2-0-aanm-1-1-adaptive-anisotropic-network-model-web-server.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://anm.csb.pitt.edu/anmdocs/Documentation2.1.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btu847", "pmid": "25568280", "pmcid": "PMC4410662", "type": [], "version": null, "note": null, "metadata": { "title": "The anisotropic network model web server at 2015 (ANM 2.0)", "abstract": "The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein-DNA/RNA and-ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces.", "date": "2015-05-01T00:00:00Z", "citationCount": 136, "authors": [ { "name": "Eyal E." }, { "name": "Lum G." }, { "name": "Bahar I." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.csb.pitt.edu/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:49Z", "lastUpdate": "2024-11-25T14:17:12.623733Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AodPred", "description": "This tool was developed to identify antioxidant proteins based on the sequence information.", "homepage": "http://lin.uestc.edu.cn/server/AntioxiPred", "biotoolsID": "aodpred", "biotoolsCURIE": "biotools:aodpred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0474", "term": "Protein structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/aodpred-identifying-antioxidant-proteins-by-using-optimal-dipeptide-compositions.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://lin.uestc.edu.cn/server/Aod/readme", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s12539-015-0124-9", "pmid": "26345449", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions", "abstract": "Antioxidant proteins are a kind of molecules that can terminate cellular and DNA damages caused by free radical intermediates. The use of antioxidant proteins for prevention of diseases has been intensively studied in recent years. Thus, accurate identification of antioxidant proteins is essential for understanding their roles in pharmacology. In this study, a support vector machine-based predictor called AodPred was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using feature selection method. It was observed by jackknife cross-validation test that AodPred can achieve an overall accuracy of 74.79 % in identifying antioxidant proteins. As a user-friendly tool, AodPred is freely accessible at http://lin.uestc.edu.cn/server/AntioxiPred. To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results.", "date": "2016-06-01T00:00:00Z", "citationCount": 45, "authors": [ { "name": "Feng P." }, { "name": "Chen W." }, { "name": "Lin H." } ], "journal": "Interdisciplinary Sciences – Computational Life Sciences" } } ], "credit": [ { "name": "Hao Lin", "email": null, "url": "http://lin.uestc.edu.cn/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:25Z", "lastUpdate": "2024-11-25T14:17:11.389141Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "apComplex", "description": "Functions to estimate a bipartite graph of protein complex membership using AP-MS data.", "homepage": "http://bioconductor.org/packages/release/bioc/html/apComplex.html", "biotoolsID": "apcomplex", "biotoolsCURIE": "biotools:apcomplex", "version": [ "2.40.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0320", "term": "Protein structure assignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Proteomics", "BioConductor" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/apComplex_2.40.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/apComplex.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bti567", "pmid": "15998662", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Local modeling of global interactome networks", "abstract": "Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity-purification/mass-spectrometry (AP-MS) technologies measure different protein-protein relationships, and issues of completeness, sensitivity and specificity fuel debate over which is best for high-throughput 'interactome' data collection. Static graphs currently used to model Y2H and AP-MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function. Results: We apply the local modeling methodology proposed by Scholtens and Gentleman (2004) to two publicly available datasets and demonstrate its uses, interpretation and limitations. Specifically, we use this technology to address four major issues pertaining to protein-protein networks. (1) We motivate the need to move from static global interactome graphs to local protein complex models. (2) We formally show that accurate local interactome models require both Y2H and AP-MS data, even in idealized situations. (3) We briefly discuss experimental design issues and how bait selection affects interpretability of results. (4) We point to the implications of local modeling for systems biology including functional annotation, new complex prediction, pathway interactivity and coordination with gene-expression data. © The Author 2005. Published by Oxford University Press. All rights reserved.", "date": "2005-09-01T00:00:00Z", "citationCount": 66, "authors": [ { "name": "Scholtens D." }, { "name": "Vidal M." }, { "name": "Gentleman R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Denise Scholtens", "email": "dscholtens@northwestern.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "bioconductor_import", "additionDate": "2017-01-17T15:04:02Z", "lastUpdate": "2024-11-25T14:17:10.116176Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "APECS", "description": "Proteomics method for intensity-based precursor ion selection, using a MALDI-TOF/TOF instrument, from a complex sample separated by 2D-LC.", "homepage": "https://trac.nbic.nl/apecs/", "biotoolsID": "apecs", "biotoolsCURIE": "biotools:apecs", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2426", "term": "Modelling and simulation" }, { "uri": "http://edamontology.org/operation_3627", "term": "Mass spectra calibration" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3524", "term": "Simulation experiment" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Python" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/apecs-intensity-based-peptide-selection.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://trac.nbic.nl/apecs/wiki#no1", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/pr1006944", "pmid": "20836568", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Apex peptide elution chain selection: A new strategy for selecting precursors in 2D-LC-MALDI-TOF/TOF experiments on complex biological samples", "abstract": "LC-MALDI provides an often overlooked opportunity to exploit the separation between LC-MS and MS/MS stages of a 2D-LC-MS-based proteomics experiment, that is, by making a smarter selection for precursor fragmentation. Apex Peptide Elution Chain Selection (APECS) is a simple and powerful method for intensity-based peptide selection in a complex sample separated by 2D-LC, using a MALDI-TOF/TOF instrument. It removes the peptide redundancy present in the adjacent first-dimension (typically strong cation exchange, SCX) fractions by constructing peptide elution profiles that link the precursor ions of the same peptide across SCX fractions. Subsequently, the precursor ion most likely to fragment successfully in a given profile is selected for fragmentation analysis, selecting on precursor intensity and absence of adjacent ions that may cofragment. To make the method independent of experiment-specific tolerance criteria, we introduce the concept of the branching factor, which measures the likelihood of false clustering of precursor ions based on past experiments. By validation with a complex proteome sample of Arabidopsis thaliana, APECS identified an equivalent number of peptides as a conventional data-dependent acquisition method but with a 35% smaller work load. Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides. © 2010 American Chemical Society.", "date": "2010-11-05T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Gandhi T." }, { "name": "Fusetti F." }, { "name": "Wiederhold E." }, { "name": "Breitling R." }, { "name": "Poolman B." }, { "name": "Permentier H.P." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.nbic.nl", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:35:51Z", "lastUpdate": "2024-11-25T14:17:08.762850Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "APEX", "description": "Absolute protein expression Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data. This technique uses machine learning algorithms to help correct for variable peptide detection related to certain peptide physicochemical properties which favor or hinder detection. A sample data set and descriptive tutorial help to acquaint users with the operation of the tool.", "homepage": "http://sourceforge.net/projects/apexqpt/", "biotoolsID": "apex", "biotoolsCURIE": "biotools:apex", "version": [ "1.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3637", "term": "Spectral counting" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantitation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0108", "term": "Protein expression" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/apex-1-1-0-quantitative-proteomics-tool.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/nbt1270", "pmid": "17187058", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation", "abstract": "We report a method for large-scale absolute protein expression measurements (APEX) and apply it to estimate the relative contributions of transcriptional- and translational-level gene regulation in the yeast and Escherichia coli proteomes. APEX relies upon correcting each protein's mass spectrometry sampling depth (observed peptide count) by learned probabilities for identifying the peptides. APEX abundances agree with measurements from controls, western blotting, flow cytometry and two-dimensional gels, as well as known correlations with mRNA abundances and codon bias, providing absolute protein concentrations across approximately three to four orders of magnitude. Using APEX, we demonstrate that 73% of the variance in yeast protein abundance (47% in E. coli) is explained by mRNA abundance, with the number of proteins per mRNA log-normally distributed about ∼5,600 (∼540 in E. coli) protein molecules/mRNA. Therefore, levels of both eukaryotic and prokaryotic proteins are set per mRNA molecule and independently of overall protein concentration, with >70% of yeast gene expression regulation occurring through mRNA-directed mechanisms. © 2007 Nature Publishing Group.", "date": "2007-01-05T00:00:00Z", "citationCount": 941, "authors": [ { "name": "Lu P." }, { "name": "Vogel C." }, { "name": "Wang R." }, { "name": "Yao X." }, { "name": "Marcotte E.M." } ], "journal": "Nature Biotechnology" } } ], "credit": [ { "name": null, "email": null, "url": "http://www.marcottelab.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-12-18T00:03:16Z", "lastUpdate": "2024-11-25T14:17:07.451861Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ArchCandy", "description": "Tool able to decode protein sequence motifs that have a potential to form amyloids.", "homepage": "http://bioinfo.montp.cnrs.fr/?r=ArchCandy", "biotoolsID": "archcandy", "biotoolsCURIE": "biotools:archcandy", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/archcandy-detect-regions-in-protein-sequences-that-have-a-potential-to-form-amyloids.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioinfo.montp.cnrs.fr/?r=ArchCandy&p=home", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jalz.2014.06.007", "pmid": "25150734", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A structure-based approach to predict predisposition to amyloidosis", "abstract": "Background: Neurodegenerative diseases and other amyloidoses are linked to the formation of amyloid fibrils. It has been shown that the ability to form these fibrils is coded by the amino acid sequence. Existing methods for the prediction of amyloidogenicity generate an unsatisfactory high number of false positives when tested against sequences of the disease-related proteins. Methods: Recently, it has been shown that the three-dimensional structure of a majority of disease-related amyloid fibrils contains a β-strand-loop-β-strand motif called β-arch. Using this information, we have developed a novel bioinformatics approach for the prediction of amyloidogenicity. Results: The benchmark results show the superior performance of our method over the existing programs. Conclusions: As genome sequencing becomes more affordable, our method provides an opportunity to create individual risk profiles for the neurodegenerative, age-related, and other diseases ushering in an era of personalized medicine. It will also be used in the large-scale analysis of proteomes to find new amyloidogenic proteins.", "date": "2015-06-01T00:00:00Z", "citationCount": 77, "authors": [ { "name": "Ahmed A.B." }, { "name": "Znassi N." }, { "name": "Chateau M.-T." }, { "name": "Kajava A.V." } ], "journal": "Alzheimer's and Dementia" } } ], "credit": [ { "name": "Andrey V. Kajava", "email": "Andrey.Kajava@crbm.cnrs.fr", "url": "http://bioinfo.montp.cnrs.fr/index.php", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:26Z", "lastUpdate": "2024-11-25T14:17:06.094012Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ArchiP", "description": "This tool detects architectures of all-β and α/β-classes", "homepage": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip", "biotoolsID": "archip", "biotoolsCURIE": "biotools:archip", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0319", "term": "Protein secondary structure assignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0082", "term": "Structure prediction" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/archip-2-1-detecting-architectures-of-all-β-and-αβ-classes.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://mouse.belozersky.msu.ru/~evgeniy/cgi-bin/proton/proton.php?subproj=archip&page=help&data=alldocs", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1142/s021972001241003x", "pmid": "22809339", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Sheep: A tool for description of β-sheets in protein 3D structures", "abstract": "The description of a protein fold is a hard problem due to significant variability of main structural units, β-sheets and α-helixes, and their mutual arrangements. An adequate description of the structural units is an important step in objective protein structure classification, which to date is based on expert judgment in a number of cases. Explicit determination and description of structural units is more complicated for β-sheets than for α-helixes due to β-sheets variability both in composition and geometry. We have developed an algorithm that can significantly modify β-sheets detected by commonly used DSSP and Stride algorithms and represent the result as a \"β-sheet map,\" a table describing certain β-sheet features. In our approach, β-sheets (rather than β-strands) are considered as holistic objects. Both hydrogen bonds and geometrical restrains are explored for the determination of β-sheets. The algorithm is implemented in SheeP program. It was tested for prediction architectures of domains from 93 well-defined all-β and α/β SCOP protein domain families, and showed 93% of correct results. The Web-service allows to detect β-sheets in a given protein structure, visualize β-sheet maps, as well as input three-dimensional structures with highlighted β-sheets and their structural features. © 2012 Imperial College Press.", "date": "2012-04-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Aksianov E." }, { "name": "Alexeevski A." } ], "journal": "Journal of Bioinformatics and Computational Biology" } } ], "credit": [ { "name": "Evgeniy Aksianov", "email": "evaksianov@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:28Z", "lastUpdate": "2024-11-25T14:17:04.676391Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ArchKI", "description": "This tool performs a structural classification of kinase loops with information of functional residues to find relationships between structure and function of classified kinase-loops.", "homepage": "http://bioinf.uab.es/cgi-bin/archki/loops.pl?class=all&set=ArchKI", "biotoolsID": "archki", "biotoolsCURIE": "biotools:archki", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0623", "term": "Gene and protein families" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/archki-classification-common-functional-loops-kinase-super-families.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://bioinf.uab.es/cgi-bin/archki/loops.pl?class=all", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/prot.20136", "pmid": "15229886", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Classification of common functional loops of kinase super-families", "abstract": "A structural classification of loops has been obtained from a set of 141 protein structures classified as kinases. A total of 1813 loops was classified into 133 subclasses (9 ββlinks, 15 ββ hairpins, 31 α-α, 46 α-β and 32 β-α). Functional information and specific features relating subclasses and function were included in the classification. Functional loops such as the P-loop (shared by different folds) or the Gly-rich-loop, among others, were classified into structural motifs. As a result, a common mechanism of catalysis and substrate binding was proved for most kinases. Additionally, the multiple-alignment of loop sequences made within each subclass was shown to be useful for comparative modeling of kinase loops. © 2004 Wiley-Liss, Inc.", "date": "2004-08-15T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Fernandez-Fuentes N." }, { "name": "Hermoso A." }, { "name": "Espadaler J." }, { "name": "Querol E." }, { "name": "Aviles F.X." }, { "name": "Oliva B." } ], "journal": "Proteins: Structure, Function and Genetics" } } ], "credit": [ { "name": null, "email": null, "url": "http://sbi.imim.es/cgi-bin/archdb/loops.pl?con=1", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:27Z", "lastUpdate": "2024-11-25T14:17:03.282188Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ArShift", "description": "Method of calculating side-chain aromatic chemical shifts from protein structures.", "homepage": "http://www-sidechain.ch.cam.ac.uk/ArShift/", "biotoolsID": "arshift", "biotoolsCURIE": "biotools:arshift", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3542", "term": "Protein secondary structure" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/arshift-structure-based-predictor-of-protein-aromatic-side-chain-proton-chemical-shifts.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www-sidechain.ch.cam.ac.uk/ArShift/", "type": [ "General" ], "note": "Downloadable PDF within homepage." } ], "publication": [ { "doi": "10.1002/anie.201101641", "pmid": "21887824", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures", "abstract": "Predicting chemical shifts: A method for the structure-based prediction of side-chain aromatic 1H chemical shifts of proteins is presented (see picture; blue structures: aromatic side chains, red spheres: aromatic hydrogen atoms). Its ability to differentiate correct structural models from incorrect ones is also demonstrated, together with its use to detect differences caused by cofactor or ligand binding, or by sequence alterations between structures. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.", "date": "2011-10-04T00:00:00Z", "citationCount": 21, "authors": [ { "name": "Sahakyan A.B." }, { "name": "Vranken W.F." }, { "name": "Cavalli A." }, { "name": "Vendruscolo M." } ], "journal": "Angewandte Chemie - International Edition" } } ], "credit": [ { "name": null, "email": null, "url": "http://www-vendruscolo.ch.cam.ac.uk/index.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:36:25Z", "lastUpdate": "2024-11-25T14:17:02.124102Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ASAPRatio", "description": "Statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments.", "homepage": "http://tools.proteomecenter.org/ASAPRatio.php", "biotoolsID": "asapratio", "biotoolsCURIE": "biotools:asapratio", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3638", "term": "SILAC" }, { "uri": "http://edamontology.org/operation_3630", "term": "Protein quantification" }, { "uri": "http://edamontology.org/operation_3741", "term": "Differential protein expression analysis" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3705", "term": "Isotope-coded protein label" }, { "uri": "http://edamontology.org/operation_3658", "term": "Statistical inference" }, { "uri": "http://edamontology.org/operation_3632", "term": "Isotopic distributions calculation" }, { "uri": "http://edamontology.org/operation_3635", "term": "Labeled quantification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_3655", "term": "pepXML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1669", "term": "P-value" }, "format": [ { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3655", "term": "pepXML" } ] }, { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [ { "uri": "http://edamontology.org/format_3747", "term": "protXML" }, { "uri": "http://edamontology.org/format_3655", "term": "pepXML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "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_2269", "term": "Statistics and probability" } ], "operatingSystem": [ "Windows" ], "language": [ "C++" ], "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": [], "documentation": [ { "url": "http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/ac034633i", "pmid": "14640741", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Automated Statistical Analysis of Protein Abundance Ratios from Data Generated by Stable-Isotope Dilution and Tandem Mass Spectrometry", "abstract": "We describe an algorithm for the automated statistical analysis of protein abundance ratios (ASAPRatio) of proteins contained in two samples. Proteins are labeled with distinct stable-isotope tags and fragmented, and the tagged peptide fragments are separated by liquid chromatography (LC) and analyzed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS). The algorithm utilizes the signals recorded for the different isotopic forms of peptides of identical sequence and numerical and statistical methods, such as Savitzky-Golay smoothing filters, statistics for weighted samples, and Dixon's test for outliers, to evaluate protein abundance ratios and their associated errors. The algorithm also provides a statistical assessment to distinguish proteins of significant abundance changes from a population of proteins of unchanged abundance. To evaluate its performance, two sets of LC-ESI-MS/MS data were analyzed by the ASAPRatio algorithm without human intervention, and the data were related to the expected and manually validated values. The utility of the ASAPRatio program was clearly demonstrated by its speed and the accuracy of the generated protein abundance ratios and by its capability to identify specific core components of the RNA polymerase II transcription complex within a high background of copurifying proteins.", "date": "2003-12-01T00:00:00Z", "citationCount": 323, "authors": [ { "name": "Li X.-J." }, { "name": "Zhang H." }, { "name": "Ranish J.A." }, { "name": "Aebersold R." } ], "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": "2017-01-17T14:51:31Z", "lastUpdate": "2024-11-25T14:17:00.893759Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AtSubP", "description": "A highly accurate subcellular localization prediction tool for annotating the Arabidopsis thaliana proteome.", "homepage": "http://bioinfo3.noble.org/AtSubP/", "biotoolsID": "atsubp", "biotoolsCURIE": "biotools:atsubp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2489", "term": "Protein subcellular localisation prediction" }, { "uri": "http://edamontology.org/operation_0267", "term": "Protein secondary structure prediction" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://bioinfo3.noble.org/AtSubP/?dowhat=Help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1104/pp.110.156851", "pmid": "20647376", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis", "abstract": "A complete map of the Arabidopsis (Arabidopsis thaliana) proteome is clearly a major goal for the plant research community in terms of determining the function and regulation of each encoded protein. Developing genome-wide prediction tools such as for localizing gene products at the subcellular level will substantially advance Arabidopsis gene annotation. To this end, we performed a comprehensive study in Arabidopsis and created an integrative support vector machine-based localization predictor called AtSubP (for Arabidopsis subcellular localization predictor) that is based on the combinatorial presence of diverse protein features, such as its amino acid composition, sequence-order effects, terminal information, Position-Specific Scoring Matrix, and similarity search-based Position-Specific Iterated-Basic Local Alignment Search Tool information. When used to predict seven subcellular compartments through a 5-fold cross-validation test, our hybrid-based best classifier achieved an overall sensitivity of 91% with high-confidence precision and Matthews correlation coefficient values of 90.9% and 0.89, respectively. Benchmarking AtSubP on two independent data sets, one from Swiss-Prot and another containing green fluorescent protein- and mass spectrometry-determined proteins, showed a significant improvement in the prediction accuracy of species-specific AtSubP over some widely used \"general\" tools such as TargetP, LOCtree, PA-SUB, MultiLoc, WoLF PSORT, Plant-PLoc, and our newly created All-Plant method. Cross-comparison of AtSubP on six nontrained eukaryotic organisms (rice [Oryza sativa], soybean [Glycine max], human [Homo sapiens], yeast [Saccharomyces cerevisiae], fruit fly [Drosophila melanogaster], and worm [Caenorhabditis elegans]) revealed inferior predictions. AtSubP significantly outperformed all the prediction tools being currently used for Arabidopsis proteome annotation and, therefore, may serve as a better complement for the plant research community. A supplemental Web site that hosts all the training/testing data sets and whole proteome predictions is available at http://bioinfo3.noble.org/AtSubP/. © 2010 American Society of Plant Biologists.", "date": "2010-01-01T00:00:00Z", "citationCount": 73, "authors": [ { "name": "Kaundal R." }, { "name": "Saini R." }, { "name": "Zhao P.X." } ], "journal": "Plant Physiology" } } ], "credit": [ { "name": "AtSubP team", "email": "bioinfo@noble.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-05-01T17:09:03Z", "lastUpdate": "2024-11-25T14:16:58.795083Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "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": "Babelomics", "description": "Integrative platform for the analysis of Transcriptomics, Proteomics and Genomics data with advanced functional profiling. It integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods.", "homepage": "http://babelomics.bioinfo.cipf.es/", "biotoolsID": "babelomics", "biotoolsCURIE": "biotools:babelomics", "version": [ "5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0277", "term": "Pathway or network comparison" }, { "uri": "http://edamontology.org/operation_3559", "term": "Ontology visualisation" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_3463", "term": "Gene expression correlation" }, { "uri": "http://edamontology.org/operation_0313", "term": "Gene expression clustering" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" } ] }, { "data": { "uri": "http://edamontology.org/data_3110", "term": "Raw microarray data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2872", "term": "ID list" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2082", "term": "Matrix" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0582", "term": "Ontology" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2884", "term": "Plot" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "ELIXIR-ES", "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/babelomics/babelomics", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/babelomics/babelomics/wiki#citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://github.com/babelomics/babelomics/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv384", "pmid": "25897133", "pmcid": "PMC4489263", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Babelomics 5.0: Functional interpretation for new generations of genomic data", "abstract": "Babelomics has been running for more than one decade offering a user-friendly interface for the functional analysis of gene expression and genomic data. Here we present its fifth release, which includes support for Next Generation Sequencing data including gene expression (RNA-seq), exome or genome resequencing. Babelomics has simplified its interface, being now more intuitive. Improved visualization options, such as a genome viewer as well as an interactive network viewer, have been implemented. New technical enhancements at both, client and server sides, makes the user experience faster and more dynamic. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a variety of tests for different experimental designs and (iii) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context. In addition to the public server, local copies of Babelomics can be downloaded and installed. Babelomics is freely available at: http://www.babelomics.org.", "date": "2015-01-01T00:00:00Z", "citationCount": 100, "authors": [ { "name": "Alonso R." }, { "name": "Salavert F." }, { "name": "Garcia-Garcia F." }, { "name": "Carbonell-Caballero J." }, { "name": "Bleda M." }, { "name": "Garcia-Alonso L." }, { "name": "Sanchis-Juan A." }, { "name": "Perez-Gil D." }, { "name": "Marin-Garcia P." }, { "name": "Sanchez R." }, { "name": "Cubuk C." }, { "name": "Hidalgo M.R." }, { "name": "Amadoz A." }, { "name": "Hernansaiz-Ballesteros R.D." }, { "name": "Aleman A." }, { "name": "Tarraga J." }, { "name": "Montaner D." }, { "name": "Medina I." }, { "name": "Dopazo J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Computational Genomics Department. Prince Felipe Research Center (CIPF)", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "http://bioinfo.cipf.es", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "cipf.es", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "babelomics@cipf.es (Francisco García)", "email": "babelomics@cipf.es", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "fgarcia@cipf.es", "additionDate": "2016-07-21T13:28:23Z", "lastUpdate": "2024-11-25T14:16:55.273772Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BAGEL3", "description": "Automated identification of genes encoding bacteriocins and (non)-bacteriocidal post-translationally modified peptides using updated bacteriocin and context protein databases. Input is single or multiple FASTA formatted files.", "homepage": "http://bagel.molgenrug.nl", "biotoolsID": "bagel3", "biotoolsCURIE": "biotools:bagel3", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3631", "term": "Peptide identification" }, { "uri": "http://edamontology.org/operation_3357", "term": "Format detection" }, { "uri": "http://edamontology.org/operation_3643", "term": "Tag-based peptide identification" }, { "uri": "http://edamontology.org/operation_0436", "term": "Coding region prediction" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkt391", "pmid": "23677608", "pmcid": "PMC3692055", "type": [], "version": null, "note": null, "metadata": { "title": "BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides.", "abstract": "Identifying genes encoding bacteriocins and ribosomally synthesized and posttranslationally modified peptides (RiPPs) can be a challenging task. Especially those peptides that do not have strong homology to previously identified peptides can easily be overlooked. Extensive use of BAGEL2 and user feedback has led us to develop BAGEL3. BAGEL3 features genome mining of prokaryotes, which is largely independent of open reading frame (ORF) predictions and has been extended to cover more (novel) classes of posttranslationally modified peptides. BAGEL3 uses an identification approach that combines direct mining for the gene and indirect mining via context genes. Especially for heavily modified peptides like lanthipeptides, sactipeptides, glycocins and others, this genetic context harbors valuable information that is used for mining purposes. The bacteriocin and context protein databases have been updated and it is now easy for users to submit novel bacteriocins or RiPPs. The output has been simplified to allow user-friendly analysis of the results, in particular for large (meta-genomic) datasets. The genetic context of identified candidate genes is fully annotated. As input, BAGEL3 uses FASTA DNA sequences or folders containing multiple FASTA formatted files. BAGEL3 is freely accessible at http://bagel.molgenrug.nl.", "date": "2013-01-01T00:00:00Z", "citationCount": 396, "authors": [ { "name": "van Heel A.J." }, { "name": "de Jong A." }, { "name": "Montalban-Lopez M." }, { "name": "Kok J." }, { "name": "Kuipers O.P." } ], "journal": "Nucleic acids research" } } ], "credit": [ { "name": "A.J. van Heel", "email": "a.j.van.heel@rug.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-25T17:08:07Z", "lastUpdate": "2024-11-25T14:16:53.063051Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BetaVoid", "description": "This software recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area.", "homepage": "http://voronoi.hanyang.ac.kr/software.htm#BetaVoidWin", "biotoolsID": "betavoid", "biotoolsCURIE": "biotools:betavoid", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0245", "term": "Protein structural motif recognition" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_2275", "term": "Molecular modelling" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/betavoid-v1-molecular-voids-via-beta-complexes-and-voronoi-diagrams.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://voronoi.hanyang.ac.kr/software.htm#BetaVoidWin", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/prot.24537", "pmid": "24677176", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "BetaVoid: Molecular voids via beta-complexes and Voronoi diagrams", "abstract": "Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta-complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center (http://voronoi.hanyang.ac.kr). © 2014 Wiley Periodicals, Inc.", "date": "2014-01-01T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Kim J.-K." }, { "name": "Cho Y." }, { "name": "Laskowski R.A." }, { "name": "Ryu S.E." }, { "name": "Sugihara K." }, { "name": "Kim D.-S." } ], "journal": "Proteins: Structure, Function and Bioinformatics" } } ], "credit": [ { "name": null, "email": null, "url": "http://voronoi.hanyang.ac.kr/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:37:22Z", "lastUpdate": "2024-11-25T14:16:51.628122Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioDrugScreen", "description": "Resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes. The targets are originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, created for this. This makes the resource highly valuable in drug discovery.", "homepage": "http://www.biodrugscore.org", "biotoolsID": "biodrugscreen", "biotoolsCURIE": "biotools:biodrugscreen", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2929", "term": "Protein fragment weight comparison" }, { "uri": "http://edamontology.org/operation_3501", "term": "Over-representation analysis" }, { "uri": "http://edamontology.org/operation_0478", "term": "Molecular docking" }, { "uri": "http://edamontology.org/operation_0482", "term": "Protein-ligand docking" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3336", "term": "Drug discovery" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0209", "term": "Medicinal chemistry" }, { "uri": "http://edamontology.org/topic_2815", "term": "Humans" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkp852", "pmid": "19923229", "pmcid": "PMC2808957", "type": [], "version": null, "note": null, "metadata": { "title": "BioDrugScreen: A computational drug design resource for ranking molecules docked to the human proteome", "abstract": "BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on 1589 human targets resulting in >3 million receptor-ligand complexes requiring >200 000 cpu-hours on the TeraGrid. The targets in BioDrugScreen originated from Human Cancer Protein Interaction Network, which we have updated, as well as the Human Druggable Proteome, which we have created for the purpose of this effort. This makes the BioDrugScreen resource highly valuable in drug discovery. The receptor-ligand complexes within the database can be ranked using standard and well-established scoring functions like AutoDock, DockScore, ChemScore, X-Score, GoldScore, DFIRE and PMF. In addition, we have scored the complexes with more intensive GBSA and PBSA approaches requiring an additional 120 000 cpu-hours on the TeraGrid. We constructed a simple interface to enable users to view top-ranking molecules and access purchasing and other information for further experimental exploration. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-18T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Li L." }, { "name": "Bum-Erdene K." }, { "name": "Baenziger P.H." }, { "name": "Rosen J.J." }, { "name": "Hemmert J.R." }, { "name": "Nellis J.A." }, { "name": "Pierce M.E." }, { "name": "Meroueh S.O." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Samy O. Meroueh", "email": "smeroueh@iupui.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-27T07:56:17Z", "lastUpdate": "2024-11-25T14:16:50.029041Z", "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": "BiopLib", "description": "Library of C routines for general programming and handling protein structure", "homepage": "http://www.bioinf.org.uk/software/bioplib/index.html", "biotoolsID": "bioplib", "biotoolsCURIE": "biotools:bioplib", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/bioptools-1-1-a-set-of-command-line-tools-for-manipulating-protein-structure.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.bioinf.org.uk/software/bioplib/bioplib/doc/html/pages.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btv482", "pmid": "26323716", "pmcid": "PMC4673973", "type": [], "version": null, "note": null, "metadata": { "title": "BiopLib and BiopTools - A C programming library and toolset for manipulating protein structure", "abstract": "We describe BiopLib, a mature C programming library for manipulating protein structure, and BiopTools, a set of command-line tools which exploit BiopLib. The library also provides a small number of functions for handling protein sequence and general purpose programming and mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. BiopTools provides facilities ranging from renumbering atoms and residues to calculation of solvent accessibility.", "date": "2015-07-03T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Porter C.T." }, { "name": "Martin A.C.R." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Dr. Andrew C.R. Martin", "email": "andrew@bioinf.org.uk", "url": "http://www.bioinf.org.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:37:44Z", "lastUpdate": "2024-11-25T14:16:47.356007Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioSunMS", "description": "Management of patients information and the analysis of peptide profiles from mass spectrometry.", "homepage": "http://biosunms.sourceforge.net/", "biotoolsID": "biosunms", "biotoolsCURIE": "biotools:biosunms", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3214", "term": "Spectral analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [], "language": [], "license": "GPL-1.0", "collectionID": [ "Proteomics" ], "maturity": null, "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://sourceforge.net/projects/biosunms/files/latest/download", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://sourceforge.net/p/biosunms/wiki/Home/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1472-6947-9-13", "pmid": "19220920", "pmcid": "PMC2654546", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "BioSunMS: A plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry", "abstract": "Background. With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis. Results. Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application. Conclusion. BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/. © 2009 Cao et al; licensee BioMed Central Ltd.", "date": "2009-01-01T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Cao Y." }, { "name": "Wang N." }, { "name": "Ying X." }, { "name": "Li A." }, { "name": "Wang H." }, { "name": "Zhang X." }, { "name": "Li W." } ], "journal": "BMC Medical Informatics and Decision Making" } } ], "credit": [ { "name": null, "email": "labs.net@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jison", "additionDate": "2018-03-06T08:13:57Z", "lastUpdate": "2024-11-25T14:16:46.069559Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Bioverse", "description": "System that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.", "homepage": "http://bioverse.compbio.washington.edu/", "biotoolsID": "bioverse", "biotoolsCURIE": "biotools:bioverse", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3455", "term": "Molecular replacement" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation inference" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkg550", "pmid": "12824406", "pmcid": "PMC168957", "type": [], "version": null, "note": null, "metadata": { "title": "Bioverse: Functional, structural and contextual annotation of proteins and proteomes", "abstract": "Functional annotation is routinely performed for large-scale genomics projects and databases. Researchers working on more specific problems, for instance on an individual pathway or complex, also need to be able to quickly, completely and accurately annotate sequences. The Bioverse sequence annotation server (http://bioverse.compbio.washington.edu) provides a web-based interface to allow users to submit protein sequences to the Bioverse framework. Sequences are functionally and structurally annotated and potential contextual annotations are provided. Researchers can also submit candidate genomes for annotation of all proteins encoded by the genome (proteome).", "date": "2003-07-01T00:00:00Z", "citationCount": 19, "authors": [ { "name": "McDermott J." }, { "name": "Samudrala R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/bti514", "pmid": "15919725", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Functional annotation from predicted protein interaction networks", "abstract": "Motivation: Progress in large-scale experimental determination of protein-protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes. Results: We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations. © The Author 2005. Published by Oxford University Press. All rights reserved.", "date": "2005-08-01T00:00:00Z", "citationCount": 46, "authors": [ { "name": "McDermott J." }, { "name": "Bumgarner R." }, { "name": "Samudrala R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gki401", "pmid": "15980482", "pmcid": "PMC1160162", "type": [], "version": null, "note": null, "metadata": { "title": "BIOVERSE: Enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes", "abstract": "We have made a number of enhancements to the previously described Bioverse web server and computational biology framework (http:// bioverse.compbio.washington.edu). In this update, we provide an overview of the new features available that include: (i) expansion of the number of organisms represented in the Bioverse and addition of new data sources and novel prediction techniques not available elsewhere, including network-based annotation; (ii) reengineering the database backend and supporting code resulting in significant speed, search and ease-of use improvements; and (iii) creation of a stateful and dynamic web application frontend to improve interface speed and usability. Integrated Java-based applications also allow dynamic visualization of real and predicted protein interaction networks. © 2005 Oxford University Press.", "date": "2005-07-01T00:00:00Z", "citationCount": 15, "authors": [ { "name": "McDermott J." }, { "name": "Guerquin M." }, { "name": "Frazier Z." }, { "name": "Chang A.N." }, { "name": "Samudrala R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1016/j.tibtech.2003.11.010", "pmid": "14757037", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Enhanced functional information from predicted protein networks", "abstract": "Experimentally derived genome-wide protein interaction networks have been useful in the elucidation of functional information that is not evident from examining individual proteins but determination of these networks is complex and time consuming. To address this problem, several computational methods for predicting protein networks in novel genomes have been developed. A recent publication by Date and Marcotte describes the use of phylogenetic profiling for elucidating novel pathways in proteomes that have not been experimentally characterized. This method, in combination with other computational methods for generating protein-interaction networks, might help identify novel functional pathways and enhance functional annotation of individual proteins.", "date": "2004-01-01T00:00:00Z", "citationCount": 18, "authors": [ { "name": "McDermott J." }, { "name": "Samudrala R." }, { "name": "Date S.V." }, { "name": "Marcotte E.M." } ], "journal": "Trends in Biotechnology" } } ], "credit": [], "owner": "ELIXIR-EE", "additionDate": "2017-02-07T13:52:13Z", "lastUpdate": "2024-11-25T14:16:41.109381Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BsFinder", "description": "Tool for predicting the binding sites for the given proteins. It is implemented in Java.", "homepage": "https://sites.google.com/site/guofeics/bsfinder", "biotoolsID": "bsfinder", "biotoolsCURIE": "biotools:bsfinder", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/bsfinder-predicting-the-binding-sites-for-the-given-proteins.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "https://sites.google.com/site/guofeics/bsfinder", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-13-s10-s2", "pmid": "22759425", "pmcid": "PMC3382440", "type": [], "version": null, "note": null, "metadata": { "title": "Computing the protein binding sites.", "abstract": "Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications including molecular docking, de novo drug design, structure identification and comparison of functional sites. Structural genomic projects are beginning to produce protein structures with unknown functions. Therefore, efficient methods are required if all these structures are to be properly annotated. Lots of methods for finding binding sites involve 3D structure comparison. Here we design a method to find protein binding sites by direct comparison of protein 3D structures. We have developed an efficient heuristic approach for finding similar binding sites from the surface of given proteins. Our approach consists of three steps: local sequence alignment, protein surface detection, and 3D structures comparison. We implement the algorithm and produce a software package that works well in practice. When comparing a complete protein with all complete protein structures in the PDB database, experiments show that the average recall value of our approach is 82% and the average precision value of our approach is also significantly better than the existing approaches. Our program has much higher recall values than those existing programs. Experiments show that all the existing approaches have recall values less than 50%. This implies that more than 50% of real binding sites cannot be reported by those existing approaches. The software package is available at http://sites.google.com/site/guofeics/bsfinder.", "date": "2012-01-01T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Guo F." }, { "name": "Wang L." } ], "journal": "BMC bioinformatics" } } ], "credit": [ { "name": "Lusheng Wang, Professor", "email": "lwang@cs.cityu.edu.hk", "url": "http://www.cs.cityu.edu.hk/~lwang/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:37:54Z", "lastUpdate": "2024-11-25T14:16:39.849815Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CAB-align", "description": "Contact area-based alignment is a flexible protein structure alignment method based on the residue-residue contact area.", "homepage": "http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html", "biotoolsID": "cab-align", "biotoolsCURIE": "biotools:cab-align", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0295", "term": "Structure alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" } ], "operatingSystem": [ "Linux" ], "language": [], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/cab-align-residue-residue-contact-area-based-alignment.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Download_files/CABalign/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pone.0141440", "pmid": "26502070", "pmcid": "PMC4621035", "type": [], "version": null, "note": null, "metadata": { "title": "CAB-align: A flexible protein structure alignment method based on the residue-residue contact area", "abstract": "Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CABalign), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-ofthe-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm. kitasato-u.ac.jp/bmd/bmd/Publications.html.", "date": "2015-10-26T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Terashi G." }, { "name": "Takeda-Shitaka M." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Mayuko Takeda-Shitaka", "email": "shitakam@pharm.kitasato-u.ac.jp", "url": "http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Welcome.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:37:57Z", "lastUpdate": "2024-11-25T14:16:38.654925Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CCCP", "description": "Coiled-Coil Crick Parameterization is a programs for fitting Crick parameters to coiled-coil structures and generations of ideal structures from parameters.", "homepage": "http://www.grigoryanlab.org/cccp/", "biotoolsID": "cccp", "biotoolsCURIE": "biotools:cccp", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_2814", "term": "Protein structure analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "MATLAB" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.mybiosoftware.com/cccp-coiled-coil-crick-parameterization.html", "type": [ "Software catalogue" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.grigoryanlab.org/cccp/sourceForDownload/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.jmb.2010.08.058", "pmid": "20932976", "pmcid": "PMC3052747", "type": [], "version": null, "note": null, "metadata": { "title": "Probing designability via a generalized model of helical bundle geometry", "abstract": "Because the space of folded protein structures is highly degenerate, with recurring secondary and tertiary motifs, methods for representing protein structure in terms of collective physically relevant coordinates are of great interest. By collapsing structural diversity to a handful of parameters, such methods can be used to delineate the space of designable structures (i.e., conformations that can be stabilized with a large number of sequences)-a crucial task for de novo protein design. We first demonstrate this on natural α-helical coiled coils using the Crick parameterization. We show that over 95% of known coiled-coil structures are within A1-Å Cα root mean square deviation of a Crick-ideal backbone. Derived parameters show that natural geometric space of coiled coils is highly restricted and can be represented by \"allowed\" conformations amidst a potential continuum of conformers. Allowed structures have (1) restricted axial offsets between helices, which differ starkly between parallel and anti-parallel structures; (2) preferred superhelical radii, which depend linearly on the oligomerization state; (3) pronounced radius-dependent a- and d-position amino acid propensities; and (4) discrete angles of rotation of helices about their axes, which are surprisingly independent of oligomerization state or orientation. In all, we estimate the space of designable coiled-coil structures to be reduced at least 160-fold relative to the space of geometrically feasible structures. To extend the benefits of structural parameterization to other systems, we developed a general mathematical framework for parameterizing arbitrary helical structures, which reduces to the Crick parameterization as a special case. The method is successfully validated on a set of non-coiled-coil helical bundles, frequent in channels and transporter proteins, which show significant helix bending but not supercoiling. Programs for coiled-coil parameter fitting and structure generation are provided via a web interface at http://www. gevorggrigoryan.com/cccp/, and code for generalized helical parameterization is available upon request. © 2010 Elsevier Ltd. All rights reserved.", "date": "2011-01-01T00:00:00Z", "citationCount": 172, "authors": [ { "name": "Grigoryan G." }, { "name": "Degrado W.F." } ], "journal": "Journal of Molecular Biology" } } ], "credit": [ { "name": "G. Grigoryan", "email": "gevorg.grigoryan@dartmouth.edu", "url": "http://www.grigoryanlab.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "mbs_import", "additionDate": "2017-08-03T18:38:11Z", "lastUpdate": "2024-11-25T14:16:37.390607Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CIPRO 2.5", "description": "The Ciona intestinalis protein database is an integrated protein database for the tunicate species C. intestinalis. The database collects published data as well as unique information from unpublished experimental data at various developmental stages, curated annotation data and various bioinformatic data. Homologs in humans and major model organisms are included. Annotations are open to evaluation by users through the CIPRO website.", "homepage": "http://cipro.ibio.jp/2.5", "biotoolsID": "cipro_2.5", "biotoolsCURIE": "biotools:cipro_2.5", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0477", "term": "Protein modelling" }, { "uri": "http://edamontology.org/operation_0313", "term": "Gene expression clustering" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3092", "term": "Protein feature detection" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "Perl" ], "license": null, "collectionID": [ "Proteomics" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://cipro.ibio.jp/current/#Help|FAQ", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkq1144", "pmid": "21071393", "pmcid": "PMC3013717", "type": [], "version": null, "note": null, "metadata": { "title": "CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality", "abstract": "The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includesoriginal large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite ofdevelopmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and geneexpression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analysesat various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a communitysupported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http:// cipro.ibio.jp/2.5. © The Author(s) 2010.", "date": "2011-01-01T00:00:00Z", "citationCount": 28, "authors": [ { "name": "Endo T." }, { "name": "Ueno K." }, { "name": "Yonezawa K." }, { "name": "Mineta K." }, { "name": "Hotta K." }, { "name": "Satou Y." }, { "name": "Yamada L." }, { "name": "Ogasawara M." }, { "name": "Takahashi H." }, { "name": "Nakajima A." }, { "name": "Nakachi M." }, { "name": "Nomura M." }, { "name": "Yaguchi J." }, { "name": "Sasakura Y." }, { "name": "Yamasaki C." }, { "name": "Sera M." }, { "name": "Yoshizawa A.C." }, { "name": "Imanishi T." }, { "name": "Taniguchi H." }, { "name": "Inaba K." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "T. Endo", "email": "endo@ibio.jp", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-30T21:27:43Z", "lastUpdate": "2024-11-25T14:16:36.107067Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }