{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,3,6]],"date-time":"2023-03-06T11:14:59Z","timestamp":1678101299876},"reference-count":43,"publisher":"World Scientific Pub Co Pte Lt","issue":"06","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:p> A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. This system, which we call the affinity evaluation and prediction (AEP) system, was used to evaluate the interaction between 20 protein pairs. The system first executes a \"round robin\" shape complementarity search of the target protein group, and evaluates the interaction of the complex structures obtained by shape complementarity search. These complex structures are selected by using a statistical procedure that we developed called \"grouping\". At a low prevalence of 5.0%, our AEP system predicted protein\u2013protein interaction with 65.0% recall, 15.1% precision, 80.0% accuracy, and had an area under the curve (AUC) of 0.74. By optimizing the grouping process, our AEP system successfully predicted 13 protein pairs (among 20 pairs) that were biologically significant combinations. Our ultimate goal is to construct an affinity database that will provide crucial information obtained using our AEP system to cell biologists and drug designers. <\/jats:p>","DOI":"10.1142\/s0219720008003904","type":"journal-article","created":{"date-parts":[[2008,12,17]],"date-time":"2008-12-17T11:31:28Z","timestamp":1229513488000},"page":"1133-1156","source":"Crossref","is-referenced-by-count":6,"title":["DEVELOPMENT OF AN AFFINITY EVALUATION AND PREDICTION SYSTEM BY USING THE SHAPE COMPLEMENTARITY CHARACTERISTIC BETWEEN PROTEINS"],"prefix":"10.1142","volume":"06","author":[{"given":"KOKI","family":"TSUKAMOTO","sequence":"first","affiliation":[{"name":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"TATSUYA","family":"YOSHIKAWA","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan"},{"name":"Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"YUICHIRO","family":"HOURAI","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"KAZUHIKO","family":"FUKUI","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"YUTAKA","family":"AKIYAMA","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.1.13"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/18.suppl_2.S249"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2005.06.006"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1038\/nature04209"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1038\/nature05649"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-7-r130"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E07-06-0536"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1126\/science.1090289"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-12-r96"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1038\/35051615"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.suppl_1.S296"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1016\/S0014-5793(03)00456-3"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(02)00285-3"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti512"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti366"},{"key":"rf16","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1007\/978-3-540-74742-0_84","volume":"4742","author":"Nukada A.","year":"2007"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10389"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10388"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti229"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20576"},{"key":"rf21","doi-asserted-by":"publisher","DOI":"10.1007\/11535409_71"},{"key":"rf22","series-title":"Lecture Notes on Computer Science","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1007\/3-540-45350-4_14","volume":"1924","author":"Vuduc R.","year":"2000"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20560"},{"key":"rf24","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10390"},{"key":"rf25","doi-asserted-by":"publisher","DOI":"10.1038\/374183a0"},{"key":"rf26","doi-asserted-by":"publisher","DOI":"10.1038\/77950"},{"key":"rf27","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(97)00183-4"},{"key":"rf28","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/42523","volume":"387","author":"Gao G. F.","journal-title":"Nature"},{"key":"rf29","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(00)00174-X"},{"key":"rf30","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(01)00315-4"},{"key":"rf31","doi-asserted-by":"publisher","DOI":"10.1038\/26773"},{"key":"rf33","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(98)00092-6"},{"key":"rf34","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0995-752"},{"key":"rf35","doi-asserted-by":"publisher","DOI":"10.1126\/science.277.5324.333"},{"key":"rf36","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.3812"},{"key":"rf37","doi-asserted-by":"publisher","DOI":"10.1126\/science.8140419"},{"key":"rf38","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/20.12.2995"},{"key":"rf39","doi-asserted-by":"publisher","DOI":"10.1126\/science.286.5444.1579"},{"key":"rf40","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)01131-2"},{"key":"rf41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.192368699"},{"key":"rf42","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(01)00316-6"},{"key":"rf43","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M202327200"},{"key":"rf44","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80774-6"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720008003904","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T02:42:04Z","timestamp":1565145724000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720008003904"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,12]]},"references-count":43,"journal-issue":{"issue":"06","published-online":{"date-parts":[[2011,11,21]]},"published-print":{"date-parts":[[2008,12]]}},"alternative-id":["10.1142\/S0219720008003904"],"URL":"https:\/\/doi.org\/10.1142\/s0219720008003904","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,12]]}}}