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

TLDR

AutoDock Vina is introduced as a new program for molecular docking and virtual screening. The program automatically generates grid maps and clusters docking results, simplifying the workflow for users. AutoDock Vina delivers a two‑order‑of‑magnitude speed increase over AutoDock 4 while improving binding‑mode accuracy, and gains additional speed through multithreading on multicore machines. © 2009 Wiley Periodicals, Inc., J Comput Chem 2010.

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