title: Accelerating Virtual High-Throughput Ligand Docking: current technology and case study on a petascale supercomputer.
abstract: 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.
authors.affiliation: Genome Science and Technology, University of Tennessee, Center for Molecular Biophysics, Oak Ridge National Laboratory.
authors.forename: Sally R
authors.initials: SR
authors.lastname: Ellingson
authors.affiliation: Lombardi Comprehensive, Cancer Center, Georgetown University Medical Cntr.
authors.forename: Sivanesan
authors.initials: S
authors.lastname: Dakshanamurthy
authors.affiliation: Lombardi Comprehensive, Cancer Center, Georgetown University Medical Cntr.
authors.forename: Milton
authors.initials: M
authors.lastname: Brown
authors.affiliation: Biochemistry and Cellular and Molecular Biology, University of Tennessee, Center for Molecular Biophysics, Oak Ridge National Laboratory.
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.affiliation: Biochemistry and Cellular and Molecular Biology, University of Tennessee, Center for Molecular Biophysics, Oak Ridge National Laboratory.
authors.forename: Jerome
authors.initials: J
authors.lastname: Baudry
keywords: Automated molecular docking; Drug discovery; High-performance computing; Virtual high-throughput screening
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