{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:29:51Z","timestamp":1760956191860,"version":"3.41.2"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,4,22]],"date-time":"2023-04-22T00:00:00Z","timestamp":1682121600000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Life Science and Drug Discovery","award":["JP22ama121029j0001"],"award-info":[{"award-number":["JP22ama121029j0001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Understanding the binding site of the target protein is essential for rational drug design. Pocket detection software predicts the ligand binding site of the target protein; however, the predicted protein pockets are often excessively estimated in comparison with the actual volume of the bound ligands. This study proposes a refinement tool for the pockets predicted by an alpha sphere-based approach, Pocket to Concavity (P2C). P2C is divided into two modes: Ligand-Free (LF) and Ligand-Bound (LB) modes. The LF mode provides the shape of the deep and druggable concavity where the core scaffold can bind. The LB mode searches the deep concavity around the bound ligand. Thus, P2C is useful for identifying and designing desirable compounds in Structure-Based Drug Design (SBDD).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Pocket to Concavity is freely available at https:\/\/github.com\/genki-kudo\/Pocket-to-Concavity. This tool is implemented in Python3 and Fpocket2.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad212","type":"journal-article","created":{"date-parts":[[2023,4,22]],"date-time":"2023-04-22T17:37:30Z","timestamp":1682185050000},"source":"Crossref","is-referenced-by-count":5,"title":["Pocket to concavity: a tool for the refinement of protein\u2013ligand binding site shape from alpha spheres"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4727-7002","authenticated-orcid":false,"given":"Genki","family":"Kudo","sequence":"first","affiliation":[{"name":"Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8571, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takumi","family":"Hirao","sequence":"additional","affiliation":[{"name":"Master\u2019s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"},{"name":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryunosuke","family":"Yoshino","sequence":"additional","affiliation":[{"name":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"},{"name":"Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yasuteru","family":"Shigeta","sequence":"additional","affiliation":[{"name":"Center for Computational Sciences, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takatsugu","family":"Hirokawa","sequence":"additional","affiliation":[{"name":"Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"},{"name":"Transborder Medical Research Center, University of Tsukuba , Tsukuba, Ibaraki 305-8575, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,4,22]]},"reference":[{"key":"2023051210065597400_btad212-B1","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cag.2022.07.005","article-title":"SHREC 2022: protein\u2013ligand binding site recognition","volume":"107","author":"Gagliardi","year":"2022","journal-title":"Comput Graph (Pergamon)"},{"key":"2023051210065597400_btad212-B2","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023051210065597400_btad212-B3","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/1471-2105-10-168","article-title":"Fpocket: an open source platform for ligand pocket detection","volume":"10","author":"Le Guilloux","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051210065597400_btad212-B4","doi-asserted-by":"crossref","first-page":"1884","DOI":"10.1002\/pro.5560070905","article-title":"Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design","volume":"7","author":"Liang","year":"1998","journal-title":"Protein Sci"},{"key":"2023051210065597400_btad212-B5","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.2174\/1568026614666140929124445","article-title":"Structure-based virtual screening for drug discovery: principles, applications and recent advances","volume":"14","author":"Lionta","year":"2014","journal-title":"Curr Top Med Chem"},{"key":"2023051210065597400_btad212-B6","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nrd.2018.77","article-title":"Cryo-EM in drug discovery: achievements, limitations and prospects","volume":"17","author":"Renaud","year":"2018","journal-title":"Nat Rev Drug Discov"},{"key":"2023051210065597400_btad212-B7","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1021\/ci1000289","article-title":"Large-scale comparison of four binding site detection algorithms","volume":"50","author":"Schmidtke","year":"2010","journal-title":"J Chem Inf Model"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad212\/50066624\/btad212.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad212\/50288139\/btad212.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/4\/btad212\/50288139\/btad212.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,12]],"date-time":"2023-05-12T10:07:25Z","timestamp":1683886045000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad212\/7136640"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,4,1]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2023,4,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad212","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,4,1]]},"published":{"date-parts":[[2023,4,1]]},"article-number":"btad212"}}