idock: A multithreaded virtual screening tool for flexible ligand docking

Abstract

AutoDock Vina is a competitive protein-ligand docking tool well known for its fast execution and high accuracy. Nevertheless, when docking a massive number of ligands, Vina has to be run multiple times, repeating receptor parsing and grid maps building over and over again. There are tremendous requests for revising Vina to reuse precalculated data and incorporate built-in support for virtual screening. Hence we developed idock, inheriting from AutoDock Vina the accurate scoring function and the efficient optimization algorithm, and significantly improving the fundamental implementation and numerical model for even faster execution. idock achieves a speedup of 3.3 in terms of CPU time and a speedup of 7.5 in terms of elapsed time on average. idock is free and open source, available at https://GitHub.com/HongjianLi/idock.