{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T07:26:08Z","timestamp":1777620368211,"version":"3.51.4"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T00:00:00Z","timestamp":1682553600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R15GM122013"],"award-info":[{"award-number":["R15GM122013"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Allostery refers to the biological process by which an effector modulator binds to a protein at a site distant from the active site, known as allosteric site. Identifying allosteric sites is essential for discovering allosteric process and is considered a critical factor in allosteric drug development. To facilitate related research, we developed PASSer (Protein Allosteric Sites Server) at https:\/\/passer.smu.edu, a web application for fast and accurate allosteric site prediction and visualization. The website hosts three trained and published machine learning models: (i) an ensemble learning model with extreme gradient boosting and graph convolutional neural network, (ii) an automated machine learning model with AutoGluon\u00a0and (iii) a learning-to-rank model with LambdaMART. PASSer accepts protein entries directly from the Protein Data Bank (PDB) or user-uploaded PDB files, and can conduct predictions within seconds. The results are presented in an interactive window that displays protein and pockets\u2019 structures, as well as a table that summarizes predictions of the top three pockets with the highest probabilities\/scores. To date, PASSer has been visited over 49\u00a0000\u00a0times in over 70 countries and has executed over 6\u00a0200 jobs.<\/jats:p>","DOI":"10.1093\/nar\/gkad303","type":"journal-article","created":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T12:43:30Z","timestamp":1682599410000},"page":"W427-W431","source":"Crossref","is-referenced-by-count":63,"title":["PASSer: fast and accurate prediction of protein allosteric sites"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0186-9811","authenticated-orcid":false,"given":"Hao","family":"Tian","sequence":"first","affiliation":[{"name":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3451-5227","authenticated-orcid":false,"given":"Sian","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2754-0862","authenticated-orcid":false,"given":"Xi","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Statistical Science, Southern Methodist University , Dallas, TX 75206, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2488-0239","authenticated-orcid":false,"given":"Peng","family":"Tao","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Center for Research Computing, Center for Drug Discovery , Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75206, USA"}]}],"member":"286","published-online":{"date-parts":[[2023,4,27]]},"reference":[{"key":"2023070504574509400_B1","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1016\/j.str.2019.01.003","article-title":"Allostery in its many disguises: from theory to applications","volume":"27","author":"Wodak","year":"2019","journal-title":"Structure"},{"key":"2023070504574509400_B2","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1042\/BST0320873","article-title":"G-protein-coupled receptor allosterism: the promise and the problem(s)","volume":"32","author":"Christopoulos","year":"2004","journal-title":"Biochem. 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