{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T01:55:40Z","timestamp":1774490140435,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":342,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Predictive tools that model protein\u2013ligand binding on demand are needed to promote ligand research in an innovative drug-design environment. However, it takes considerable time and effort to develop predictive tools that can be applied to individual ligands. An automated production pipeline that can rapidly and efficiently develop user-friendly protein\u2013ligand binding predictive tools would be useful.<\/jats:p>\n               <jats:p>Results: We developed a system for automatically generating protein\u2013ligand binding predictions. Implementation of this system in a pipeline of Semantic Web technique-based web tools will allow users to specify a ligand and receive the tool within 0.5\u20131 day. We demonstrated high prediction accuracy for three machine learning algorithms and eight ligands.<\/jats:p>\n               <jats:p>Availability and implementation: The source code and web application are freely available for download at http:\/\/utprot.net. They are implemented in Python and supported on Linux.<\/jats:p>\n               <jats:p>Contact: \u00a0shimizu@bi.a.u-tokyo.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv593","type":"journal-article","created":{"date-parts":[[2015,11,7]],"date-time":"2015-11-07T02:04:32Z","timestamp":1446861872000},"page":"901-907","source":"Crossref","is-referenced-by-count":14,"title":["Automatic generation of bioinformatics tools for predicting protein\u2013ligand binding sites"],"prefix":"10.1093","volume":"32","author":[{"given":"Yusuke","family":"Komiyama","sequence":"first","affiliation":[{"name":"1 Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan and"}]},{"given":"Masaki","family":"Banno","sequence":"additional","affiliation":[{"name":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"}]},{"given":"Kokoro","family":"Ueki","sequence":"additional","affiliation":[{"name":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"}]},{"given":"Gul","family":"Saad","sequence":"additional","affiliation":[{"name":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"}]},{"given":"Kentaro","family":"Shimizu","sequence":"additional","affiliation":[{"name":"2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan"}]}],"member":"286","published-online":{"date-parts":[[2015,11,5]]},"reference":[{"key":"2023020111562361500_btv593-B1","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1016\/S0968-0004(98)01298-5","article-title":"Iterated profile searches with PSI-BLAST\u2013a tool for discovery in protein databases","volume":"23","author":"Altschul","year":"1998","journal-title":"Trends Biochem. 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