{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T03:21:04Z","timestamp":1774581664584,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,4]],"date-time":"2016-10-04T00:00:00Z","timestamp":1475539200000},"content-version":"vor","delay-in-days":1261,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,7,1]]},"DOI":"10.1093\/nar\/gkt300","type":"journal-article","created":{"date-parts":[[2013,4,23]],"date-time":"2013-04-23T07:30:37Z","timestamp":1366702237000},"page":"W292-W296","source":"Crossref","is-referenced-by-count":21,"title":["LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites"],"prefix":"10.1093","volume":"41","author":[{"given":"Zhong-Ru","family":"Xie","sequence":"first","affiliation":[]},{"given":"Chuan-Kun","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Fang-Chih","family":"Hsiao","sequence":"additional","affiliation":[]},{"given":"Adam","family":"Yao","sequence":"additional","affiliation":[]},{"given":"Ming-Jing","family":"Hwang","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2013,4,22]]},"reference":[{"key":"key\n\t\t\t\t20171013125719_gkt300-B1","doi-asserted-by":"crossref","first-page":"W469","DOI":"10.1093\/nar\/gkq406","article-title":"3DLigandSite: predicting ligand-binding sites using similar structures","volume":"38","author":"Wass","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B2","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: a unified platform for automated protein structure and function prediction","volume":"5","author":"Roy","year":"2010","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B3","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1073\/pnas.0707684105","article-title":"A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation","volume":"105","author":"Brylinski","year":"2008","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B4","doi-asserted-by":"crossref","first-page":"5313","DOI":"10.1073\/pnas.1102210108","article-title":"Evolutionary approach to predicting the binding site residues of a protein from its primary sequence","volume":"108","author":"Tseng","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B5","doi-asserted-by":"crossref","first-page":"W413","DOI":"10.1093\/nar\/gkp281","article-title":"SITEHOUND-web: a server for ligand binding site identification in protein structures","volume":"37","author":"Hernandez","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B6","doi-asserted-by":"crossref","first-page":"2083","DOI":"10.1093\/bioinformatics\/btr331","article-title":"Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction","volume":"27","author":"Zhang","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B7","doi-asserted-by":"crossref","first-page":"1908","DOI":"10.1093\/bioinformatics\/bti315","article-title":"Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites","volume":"21","author":"Laurie","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B8","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1186\/1472-6807-6-19","article-title":"LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation","volume":"6","author":"Huang","year":"2006","journal-title":"BMC Struct. Biol."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B9","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1093\/bioinformatics\/btp599","article-title":"Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B10","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1093\/bioinformatics\/btq672","article-title":"MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets","volume":"27","author":"Zhu","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B11","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1093\/bioinformatics\/bts182","article-title":"Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles","volume":"28","author":"Xie","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B12","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1186\/1471-2105-11-298","article-title":"An interaction-motif-based scoring function for protein-ligand docking","volume":"11","author":"Xie","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B13","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B14","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1002\/prot.22557","article-title":"Assessment of ligand binding residue predictions in CASP8","volume":"77","author":"Lopez","year":"2009","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B15","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1002\/prot.23174","article-title":"Assessment of ligand-binding residue predictions in CASP9","volume":"79","author":"Schmidt","year":"2011","journal-title":"Proteins"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B16","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B17"},{"key":"key\n\t\t\t\t20171013125719_gkt300-B18","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1146\/annurev-biochem-052410-090317","article-title":"The structural basis for control of eukaryotic protein kinases","volume":"81","author":"Endicott","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B19","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkr825","article-title":"Pocketome: an encyclopedia of small-molecule binding sites in 4D","volume":"40","author":"Kufareva","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20171013125719_gkt300-B20","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.tibs.2005.12.006","article-title":"Disseminating structural genomics data to the public: from a data dump to an animated story","volume":"31","author":"Abagyan","year":"2006","journal-title":"Trends Biochem. Sci."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/41\/W1\/W292\/3821989\/gkt300.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T14:41:13Z","timestamp":1522680073000},"score":1,"resource":{"primary":{"URL":"http:\/\/academic.oup.com\/nar\/article\/41\/W1\/W292\/1094035\/LISE-a-server-using-ligandinteracting-and"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,22]]},"references-count":20,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2013,4,22]]},"published-print":{"date-parts":[[2013,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkt300","relation":{},"ISSN":["1362-4962","0305-1048"],"issn-type":[{"value":"1362-4962","type":"electronic"},{"value":"0305-1048","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,7,1]]},"published":{"date-parts":[[2013,4,22]]}}}