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

O Trott, AJ Olson - Journal of computational chemistry, 2010 - Wiley Online Library
Journal of computational chemistry, 2010Wiley Online Library
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 …
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. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
Wiley Online Library