{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T18:28:38Z","timestamp":1776018518822,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identification of protein\u2013ligand binding sites is critical to protein function annotation and drug discovery. However, there is no method that could generate optimal binding site prediction for different protein types. Combination of complementary predictions is probably the most reliable solution to the problem.<\/jats:p>\n               <jats:p>Results: We develop two new methods, one based on binding-specific substructure comparison (TM-SITE) and another on sequence profile alignment (S-SITE), for complementary binding site predictions. The methods are tested on a set of 500 non-redundant proteins harboring 814 natural, drug-like and metal ion molecules. Starting from low-resolution protein structure predictions, the methods successfully recognize &amp;gt;51% of binding residues with average Matthews correlation coefficient (MCC) significantly higher (with P-value &amp;lt;10\u20139 in student t-test) than other state-of-the-art methods, including COFACTOR, FINDSITE and ConCavity. When combining TM-SITE and S-SITE with other structure-based programs, a consensus approach (COACH) can increase MCC by 15% over the best individual predictions. COACH was examined in the recent community-wide COMEO experiment and consistently ranked as the best method in last 22 individual datasets with the Area Under the Curve score 22.5% higher than the second best method. These data demonstrate a new robust approach to protein\u2013ligand binding site recognition, which is ready for genome-wide structure-based function annotations.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/zhanglab.ccmb.med.umich.edu\/COACH\/<\/jats:p>\n               <jats:p>Contact: \u00a0zhng@umich.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt447","type":"journal-article","created":{"date-parts":[[2013,8,24]],"date-time":"2013-08-24T04:09:42Z","timestamp":1377317382000},"page":"2588-2595","source":"Crossref","is-referenced-by-count":890,"title":["Protein\u2013ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment"],"prefix":"10.1093","volume":"29","author":[{"given":"Jianyi","family":"Yang","sequence":"first","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics and 2Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA"}]},{"given":"Ambrish","family":"Roy","sequence":"additional","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics and 2Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Department of Computational Medicine and Bioinformatics and 2Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA"},{"name":"1 Department of Computational Medicine and Bioinformatics and 2Department of Biological Chemistry, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,8,23]]},"reference":[{"key":"2023012810471198300_btt447-B1","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":"2023012810471198300_btt447-B2","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1074\/mcp.M400159-MCP200","article-title":"Pocketome via comprehensive identification and classification of ligand binding envelopes","volume":"4","author":"An","year":"2005","journal-title":"Mol. 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