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J Comput Chem. 2010 Jan 30;31(2):455-61. doi: 10.1002/jcc.21334.

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Author information

  • 1Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA.

Abstract

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

Copyright 2009 Wiley Periodicals, Inc.

PMID:
19499576
[PubMed - indexed for MEDLINE]
PMCID:
PMC3041641
Free PMC Article

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