{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T20:36:27Z","timestamp":1776371787282,"version":"3.51.2"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Prediction of ligand binding sites of proteins is significant as it can provide insight into biological functions and reaction mechanisms of proteins. It is also a prerequisite for protein\u2013ligand docking and an important step in structure-based drug design.<\/jats:p>\n               <jats:p>Results: We present a new algorithm, Roll, implemented in a program named POCASA, which can predict binding sites by detecting pockets and cavities of proteins with a rolling sphere. To evaluate the performance of POCASA, a test with the same data set as used in several existing methods was carried out. POCASA achieved a high success rate of 77%. In addition, the test results indicated that POCASA can predict good shapes of ligand binding sites.<\/jats:p>\n               <jats:p>Availability:A web version of POCASA is freely available at http:\/\/altair.sci.hokudai.ac.jp\/g6\/Research\/POCASA_e.html<\/jats:p>\n               <jats:p>Contact: \u00a0yao@castor.sci.hokudai.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp599","type":"journal-article","created":{"date-parts":[[2009,10,22]],"date-time":"2009-10-22T00:34:28Z","timestamp":1256171668000},"page":"46-52","source":"Crossref","is-referenced-by-count":340,"title":["Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere"],"prefix":"10.1093","volume":"26","author":[{"given":"Jian","family":"Yu","sequence":"first","affiliation":[{"name":"Graduate School of Life Science, Hokkaido University, Kita-Ku Kita-10 Nishi-8, Sapporo, 0600810, Japan"}]},{"given":"Yong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Graduate School of Life Science, Hokkaido University, Kita-Ku Kita-10 Nishi-8, Sapporo, 0600810, Japan"}]},{"given":"Isao","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Graduate School of Life Science, Hokkaido University, Kita-Ku Kita-10 Nishi-8, Sapporo, 0600810, Japan"}]},{"given":"Min","family":"Yao","sequence":"additional","affiliation":[{"name":"Graduate School of Life Science, Hokkaido University, Kita-Ku Kita-10 Nishi-8, Sapporo, 0600810, Japan"}]}],"member":"286","published-online":{"date-parts":[[2009,10,21]]},"reference":[{"key":"2023012507531208900_B1","first-page":"31","article-title":"Comprehensive identification of \u201cdruggable\u201d protein ligand binding sites","volume":"15","author":"An","year":"2004","journal-title":"Genome Informatics"},{"key":"2023012507531208900_B2","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.jmb.2005.06.047","article-title":"Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interface","volume":"351","author":"Ben-Shimon","year":"2005","journal-title":"J. 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