Accelerating virtual high-throughput ligand docking: Screening one million compounds using a petascale supercomputer

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

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

We describe a case study of using a task-parallel MPI version of Autodock4 [1,3] 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.

Original languageEnglish
Title of host publicationECMLS 2012 - 3rd International Emerging Computational Methods for the Life Sciences Workshop
Pages33-37
Number of pages5
DOIs
StatePublished - 2012
Event3rd International Emerging Computational Methods for the Life Sciences Workshop, ECMLS 2012 - Delft, Netherlands
Duration: Jun 18 2012Jun 18 2012

Publication series

NameECMLS 2012 - 3rd International Emerging Computational Methods for the Life Sciences Workshop

Conference

Conference3rd International Emerging Computational Methods for the Life Sciences Workshop, ECMLS 2012
Country/TerritoryNetherlands
CityDelft
Period6/18/126/18/12

Keywords

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

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Theoretical Computer Science

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