Accelerating virtual high-throughput ligand docking: Current technology and case study on a petascale supercomputer

Sally R. Ellingson; Sivanesan Dakshanamurthy; Milton Brown; Jeremy C. Smith; Jerome Baudry

doi:10.1002/cpe.3070

Accelerating virtual high-throughput ligand docking: Current technology and case study on a petascale supercomputer

Sally R. Ellingson, Sivanesan Dakshanamurthy, Milton Brown, Jeremy C. Smith, Jerome Baudry

Internal Medicine

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11 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1268-1277
Number of pages	10
Journal	Concurrency Computation Practice and Experience
Volume	26
Issue number	6
DOIs	https://doi.org/10.1002/cpe.3070
State	Published - Apr 25 2014

Keywords

automated molecular docking
drug discovery
high-performance computing
virtual high-throughput screening

ASJC Scopus subject areas

Theoretical Computer Science
Software
Computer Science Applications
Computer Networks and Communications
Computational Theory and Mathematics

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10.1002/cpe.3070

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AU - Baudry, Jerome

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Accelerating virtual high-throughput ligand docking: Current technology and case study on a petascale supercomputer

Abstract

Keywords

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