{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T15:00:21Z","timestamp":1776092421807,"version":"3.50.1"},"reference-count":157,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,8,31]],"date-time":"2018-08-31T00:00:00Z","timestamp":1535673600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institute of General Medical Sciences of the National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM119524"],"award-info":[{"award-number":["R35GM119524"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,27]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Interactions between proteins and small molecules are critical for biological functions. These interactions often occur in small cavities within protein structures, known as ligand-binding pockets. Understanding the physicochemical qualities of binding pockets is essential to improve not only our basic knowledge of biological systems, but also drug development procedures. In order to quantify similarities among pockets in terms of their geometries and chemical properties, either bound ligands can be compared to one another or binding sites can be matched directly. Both perspectives routinely take advantage of computational methods including various techniques to represent and compare small molecules as well as local protein structures. In this review, we survey 12 tools widely used to match pockets. These methods are divided into five categories based on the algorithm implemented to construct binding-site alignments. In addition to the comprehensive analysis of their algorithms, test sets and the performance of each method are described. We also discuss general pharmacological applications of computational pocket matching in drug repurposing, polypharmacology and side effects. Reflecting on the importance of these techniques in drug discovery, in the end, we elaborate on the development of more accurate meta-predictors, the incorporation of protein flexibility and the integration of powerful artificial intelligence technologies such as deep learning.<\/jats:p>","DOI":"10.1093\/bib\/bby078","type":"journal-article","created":{"date-parts":[[2018,8,3]],"date-time":"2018-08-03T20:16:44Z","timestamp":1533327404000},"page":"2167-2184","source":"Crossref","is-referenced-by-count":44,"title":["Binding site matching in rational drug design: algorithms and applications"],"prefix":"10.1093","volume":"20","author":[{"given":"Misagh","family":"Naderi","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey Mitchell","family":"Lemoine","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA"},{"name":"Division of Computer Science and Engineering, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajiv Gandhi","family":"Govindaraj","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Omar Zade","family":"Kana","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei Pan","family":"Feinstein","sequence":"additional","affiliation":[{"name":"High-Performance Computing, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Brylinski","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA"},{"name":"Center for Computation & Technology, Louisiana State University, Baton Rouge, LA 70803, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,31]]},"reference":[{"key":"2020011102330276300_ref1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1586\/ecp.12.74","article-title":"Polypharmacology: drug discovery for the future","volume":"6","author":"Reddy","year":"2013","journal-title":"Expert Rev Clin Pharmacol"},{"key":"2020011102330276300_ref2","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1039\/C3MB70503J","article-title":"Exploring a structural protein-drug interactome for new therapeutics in lung 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