Accelerating virtual high‐throughput ligand docking: current technology and case study on a petascale supercomputer

In this paper, we give the current state of high‐throughput virtual screening. We describe a case study of using a task‐parallel Message Passing Interface version of AutoDock4 to run a virtual high‐throughput screen of one million compounds on the Jaguar Cray XK6 Supercomputer at Oak Ridge National Laboratory. We include a description of scripts developed to increase the efficiency of the predocking file preparation and postdocking analysis. A detailed tutorial, scripts, and source code for this Message Passing Interface version of AutoDock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm. Copyright © 2013 John Wiley & Sons, Ltd.

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