{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T23:09:47Z","timestamp":1762297787072},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0JDet is a multiplatform application written in Java. It is freely available, including the source code, at http:\/\/csbg.cnb.csic.es\/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available.<\/jats:p>\n               <jats:p>Contact: \u00a0pazos@cnb.csic.es<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr688","type":"journal-article","created":{"date-parts":[[2011,12,11]],"date-time":"2011-12-11T01:23:20Z","timestamp":1323566600000},"page":"584-586","source":"Crossref","is-referenced-by-count":23,"title":["JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures"],"prefix":"10.1093","volume":"28","author":[{"given":"Thilo","family":"Muth","sequence":"first","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]},{"given":"Juan A.","family":"Garc\u00eda-Mart\u00edn","sequence":"additional","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]},{"given":"Antonio","family":"Rausell","sequence":"additional","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]},{"given":"David","family":"Juan","sequence":"additional","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]},{"given":"Florencio","family":"Pazos","sequence":"additional","affiliation":[{"name":"1 Computational Systems Biology Group, National Center for Biotechnology (CNB-CSIC), 28049 Madrid, 2Department of Plant Molecular Genetics (CNB-CSIC) and 3Structural Biology and Biocomputing Programme (CNIO), 28029 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2011,12,9]]},"reference":[{"key":"2023012512183065300_B1","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1006\/jmbi.2000.4474","article-title":"ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information","volume":"307","author":"Armon","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012512183065300_B2","doi-asserted-by":"crossref","first-page":"17763","DOI":"10.1074\/jbc.274.25.17763","article-title":"Effector recognition by the small GTP-binding proteins Ras and Ral","volume":"274","author":"Bauer","year":"1999","journal-title":"J. Biol. Chem."},{"key":"2023012512183065300_B3","doi-asserted-by":"crossref","first-page":"W110","DOI":"10.1093\/nar\/gkl203","article-title":"TreeDet: a web server to explore sequence space","volume":"34","author":"Carro","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512183065300_B4","doi-asserted-by":"crossref","first-page":"9058","DOI":"10.1074\/jbc.M209999200","article-title":"Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition. Mutation of methionine 593 abolishes malonyl-CoA inhibition","volume":"278","author":"Morillas","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2023012512183065300_B5","doi-asserted-by":"crossref","first-page":"15","DOI":"10.2174\/157489306775330633","article-title":"Computational prediction of functionally important regions in proteins","volume":"1","author":"Pazos","year":"2006","journal-title":"Curr. Bioinformatics"},{"key":"2023012512183065300_B6","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1093\/bioinformatics\/btl104","article-title":"Phylogeny-independent detection of functional residues","volume":"22","author":"Pazos","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012512183065300_B7","doi-asserted-by":"crossref","first-page":"1995","DOI":"10.1073\/pnas.0908044107","article-title":"Protein interactions and ligand binding: from protein subfamilies to functional specificity","volume":"107","author":"Rausell","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512183065300_B8","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1002\/prot.10146","article-title":"Scoring residue conservation","volume":"48","author":"Valdar","year":"2002","journal-title":"Proteins"},{"key":"2023012512183065300_B9","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2013a multiple sequence alignment editor and analysis workbench","volume":"25","author":"Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012512183065300_B10","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/0022-5193(65)90083-4","article-title":"Molecules as documents of evolutionary history","volume":"8","author":"Zuckerkandl","year":"1965","journal-title":"J. Theor. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/4\/584\/48879417\/bioinformatics_28_4_584.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/4\/584\/48879417\/bioinformatics_28_4_584.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:01:13Z","timestamp":1674658873000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/4\/584\/211857"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,12,9]]},"references-count":10,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2012,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr688","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,2,15]]},"published":{"date-parts":[[2011,12,9]]}}}