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

Research output: Contribution to journalArticlepeer-review

13 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 languageEnglish
Pages (from-to)1268-1277
Number of pages10
JournalConcurrency Computation Practice and Experience
Volume26
Issue number6
DOIs
StatePublished - 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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