{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T00:31:56Z","timestamp":1776817916632,"version":"3.51.2"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2389,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation.<\/jats:p>\n               <jats:p>Results: An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein\u2013protein, protein\u2013small ligand and protein\u2013DNA binding sites.<\/jats:p>\n               <jats:p>Availability: The software is available, as a web tool, free of charge for academic users at http:\/\/probis.cmm.ki.si<\/jats:p>\n               <jats:p>Contact: \u00a0dusa@cmm.ki.si<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq100","type":"journal-article","created":{"date-parts":[[2010,3,21]],"date-time":"2010-03-21T00:13:02Z","timestamp":1269130382000},"page":"1160-1168","source":"Crossref","is-referenced-by-count":249,"title":["ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment"],"prefix":"10.1093","volume":"26","author":[{"given":"Janez","family":"Konc","sequence":"first","affiliation":[{"name":"1 National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana and 2 University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia"}]},{"given":"Du\u0161anka","family":"Jane\u017ei\u010d","sequence":"additional","affiliation":[{"name":"1 National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana and 2 University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia"},{"name":"1 National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana and 2 University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagolja\u0161ka 8, 6000 Koper, Slovenia"}]}],"member":"286","published-online":{"date-parts":[[2010,3,19]]},"reference":[{"key":"2023012508073253700_B1","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1016\/S0076-6879(96)66029-7","article-title":"Local alignment statistics","volume":"266","author":"Altschul","year":"1996","journal-title":"Methods Enzymol."},{"key":"2023012508073253700_B2","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":"2023012508073253700_B3","doi-asserted-by":"crossref","first-page":"W565","DOI":"10.1093\/nar\/gkp405","article-title":"MolLoc: a web tool for the local structural alignment of molecular surfaces","volume":"37","author":"Angaran","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012508073253700_B4","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-9-S2-S2","article-title":"FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures","volume":"9","author":"Ausiello","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012508073253700_B5","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1107\/S0907444902003451","article-title":"The protein data bank","volume":"D58","author":"Berman","year":"2002","journal-title":"Acta Crystallogr. 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