1001 Ways to run AutoDock Vina for virtual screening.

ABSTRACT: Large-scale computing technologies have enabled high-throughput virtual screening involving thousands to millions of drug candidates. It is not trivial, however, for biochemical scientists to evaluate the technical alternatives and their implications for running such large experiments. Besides experience with the molecular docking tool itself, the scientist needs to learn how to run it on high-performance computing (HPC) infrastructures, and understand the impact of the choices made. Here, we review such considerations for a specific tool, AutoDock Vina, and use experimental data to illustrate the following points: (1) an additional level of parallelization increases virtual screening throughput on a multi-core machine; (2) capturing of the random seed is not enough (though necessary) for

SUBMITTER: Jaghoori MM 

PROVIDER: S-EPMC4801993 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature