{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T06:53:47Z","timestamp":1776322427450,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina (\u2018Vina\u2019) is a widely used docking tool with parallelization for speed. QuickVina (\u2018QVina 1\u2019) then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina (\u2018QVina 2\u2019) that inherits both the speed of QVina 1 and the reliability of the original Vina.<\/jats:p><jats:p>Results: We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina (i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58\u2009kcal\/mol. On the same dataset, GOLD produced RMSD smaller than 2\u2009\u00c5 on 56.9% of the data while QVina 2 attained 63.1%.<\/jats:p><jats:p>Availability and implementation: The C++ source code of QVina 2 is available at (www.qvina.org).<\/jats:p><jats:p>Contact: \u00a0aalhossary@pmail.ntu.edu.sg<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv082","type":"journal-article","created":{"date-parts":[[2015,2,26]],"date-time":"2015-02-26T15:34:19Z","timestamp":1424964859000},"page":"2214-2216","source":"Crossref","is-referenced-by-count":312,"title":["Fast, accurate, and reliable molecular docking with QuickVina 2"],"prefix":"10.1093","volume":"31","author":[{"given":"Amr","family":"Alhossary","sequence":"first","affiliation":[{"name":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"}]},{"given":"Stephanus Daniel","family":"Handoko","sequence":"additional","affiliation":[{"name":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"}]},{"given":"Yuguang","family":"Mu","sequence":"additional","affiliation":[{"name":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"}]},{"given":"Chee-Keong","family":"Kwoh","sequence":"additional","affiliation":[{"name":"1 School of Computer Engineering, Nanyang Technological University, Singapore 639798, 2School of Information Systems, Singapore Management University, Singapore 188065, and 3School of Biological Sciences, Nanyang Technological University, Singapore 637551"}]}],"member":"286","published-online":{"date-parts":[[2015,2,24]]},"reference":[{"key":"2023020202144586400_btv082-B1","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1021\/ci9000053","article-title":"Comparative assessment of scoring functions on a diverse test set","volume":"49","author":"Cheng","year":"2009","journal-title":"J. Chem. Inform. Model."},{"key":"2023020202144586400_btv082-B2","first-page":"1266","article-title":"QuickVina: accelerating AutoDock Vina using gradient-based heuristics for global optimization, IEEE\/ACM Trans","volume":"9","author":"Handoko","year":"2012","journal-title":"Comput. Biol. Bioinform."},{"key":"2023020202144586400_btv082-B3","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J","volume":"31","author":"Trott","year":"2010","journal-title":"Comput. Chem."},{"key":"2023020202144586400_btv082-B4","doi-asserted-by":"crossref","first-page":"4111","DOI":"10.1021\/jm048957q","article-title":"The PDBbind database: methodologies and updates","volume":"48","author":"Wang","year":"2005","journal-title":"J. Med. Chem."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2214\/49034896\/bioinformatics_31_13_2214.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/13\/2214\/49034896\/bioinformatics_31_13_2214.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T12:28:55Z","timestamp":1717763335000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/13\/2214\/195750"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,2,24]]},"references-count":4,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2015,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv082","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,7,1]]},"published":{"date-parts":[[2015,2,24]]}}}