Accelerating virtual high‐throughput ligand docking: current technology and case study on a petascale supercomputer
Sally R. Ellingson, Sivanesan Dakshanamurthy, Milton L. Brown, Jeremy C. Smith, Jerome Y. Baudry · Concurrency and Computation Practice and Experience · 2013
In this paper we give the current state of high-throughput virtual screening. We describe a case study of using a task-parallel MPI (Message Passing Interface) version of Autodock4 [1], [2] 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 MPI version of Autodock4 are available online at http://www.bio.utk.edu/baudrylab/autodockmpi.htm.