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Binding pose prediction has been improved compared to the earlier version by the efficient generation of high\u2010quality initial conformations for CSA using a predocking method based on a beta\u2010complex derived from the Voronoi diagram of receptor atoms. Binding affinity prediction has also been enhanced by using the optimal combination of energy components, while taking into consideration the energy of the unbound ligand state. The new version has been tested in terms of binding mode prediction, binding affinity prediction, and virtual screening on several benchmark sets, showing improved performance over the previous version and AutoDock, on which the GalaxyDock energy function is based. GalaxyDock2 also performs better than or comparable to other state\u2010of\u2010the\u2010art docking programs. GalaxyDock2 is freely available at <jats:ext-link xmlns:xlink=\"https:\/\/linproxy.fan.workers.dev:443\/http\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/linproxy.fan.workers.dev:443\/http\/galaxy.seoklab.org\/softwares\/galaxydock.html\">https:\/\/linproxy.fan.workers.dev:443\/http\/galaxy.seoklab.org\/softwares\/galaxydock.html<\/jats:ext-link>. \u00a9 2013 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.23438","type":"journal-article","created":{"date-parts":[[2013,10,11]],"date-time":"2013-10-11T22:09:55Z","timestamp":1381529395000},"page":"2647-2656","source":"Crossref","is-referenced-by-count":83,"title":["GalaxyDock2: Protein\u2013ligand docking using beta\u2010complex and global optimization"],"prefix":"10.1002","volume":"34","author":[{"given":"Woong\u2010Hee","family":"Shin","sequence":"first","affiliation":[{"name":"Department of Chemistry Seoul National University Seoul 151\u2010747 Republic of Korea"}]},{"given":"Jae\u2010Kwan","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Industrial Engineering Hanyang University Seoul 133\u2010791 Republic of Korea"}]},{"given":"Deok\u2010Soo","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Industrial Engineering Hanyang University Seoul 133\u2010791 Republic of Korea"}]},{"given":"Chaok","family":"Seok","sequence":"additional","affiliation":[{"name":"Department of Chemistry Seoul National University Seoul 151\u2010747 Republic of Korea"}]}],"member":"311","published-online":{"date-parts":[[2013,9,24]]},"reference":[{"key":"e_1_2_5_1_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm060999m"},{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21082"},{"key":"e_1_2_5_3_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0897"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci1001982"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/jmr.1077"},{"key":"e_1_2_5_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21905"},{"key":"e_1_2_5_8_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci300342z"},{"key":"e_1_2_5_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(19970715)18:9<1222::AID-JCC10>3.0.CO;2-7"},{"key":"e_1_2_5_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/1074-5521(95)90050-0"},{"key":"e_1_2_5_11_1","doi-asserted-by":"publisher","DOI":"10.1110\/ps.062658307"},{"key":"e_1_2_5_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cad.2010.06.004"},{"key":"e_1_2_5_13_1","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.2011.10507384"},{"key":"e_1_2_5_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci9000053"},{"key":"e_1_2_5_15_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci600426e"},{"key":"e_1_2_5_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1093-3263(98)00008-4"},{"key":"e_1_2_5_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(02)00344-5"},{"key":"e_1_2_5_18_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm061277y"},{"key":"e_1_2_5_19_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20634"},{"key":"e_1_2_5_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj039"},{"key":"e_1_2_5_21_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21844"},{"key":"e_1_2_5_22_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"e_1_2_5_23_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci049641u"},{"key":"e_1_2_5_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_5_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts395"},{"key":"e_1_2_5_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(93)87010-3"},{"key":"e_1_2_5_27_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm000375v"},{"key":"e_1_2_5_28_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm800217k"},{"key":"e_1_2_5_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm030363k"},{"key":"e_1_2_5_30_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm049092j"},{"key":"e_1_2_5_31_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm051139t"},{"key":"e_1_2_5_32_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci900419k"},{"key":"e_1_2_5_33_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-225"},{"key":"e_1_2_5_34_1","unstructured":"SYBYL 8.1; Tripos International St. Louis MO 2008."},{"key":"e_1_2_5_35_1","doi-asserted-by":"publisher","DOI":"10.1016\/0305-0548(93)E0014-K"},{"key":"e_1_2_5_36_1","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0360-8352(03)00077-9","volume":"45","author":"Park B. 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