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Grid enabled high throughput virtual screening against four different targets implicated in malaria.

Jean Salzemann1, Vinod Kasam, Nicolas Jacq

  • 1Laboratoire de Physique Corpusculaire, 63177 Aubière cedex, France.

Studies in Health Technology and Informatics
|May 4, 2007
PubMed
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Computational grids efficiently generated over 140 million molecular docking simulations for drug discovery. This high-throughput approach utilized thousands of CPUs, demonstrating the power of grid computing for large-scale biological data production.

Area of Science:

  • Computational biology
  • Bioinformatics
  • Drug discovery

Background:

  • Previous data challenges on malaria and avian flu demonstrated the utility of computational grids.
  • The WISDOM (Worldwide Information Systems for the Discovery of Molecules) production environment has been refined through experience.

Purpose of the Study:

  • To demonstrate the efficient use of computational grids for high-throughput molecular docking.
  • To generate a massive dataset of molecular docking results using available grid infrastructures.

Main Methods:

  • Utilized a computational grid infrastructure with thousands of CPUs worldwide.
  • Employed the FlexX commercial docking software for molecular docking.
  • Docked the entire ZINC database against four distinct biological targets.

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Main Results:

  • Achieved at least 140 million molecular dockings over 2.5 months.
  • Maintained an average throughput of nearly 80,000 dockings per hour.
  • Successfully deployed and utilized the FlexX software in a fault-tolerant manner on the grid.

Conclusions:

  • Computational grids are highly effective for producing massive datasets in drug discovery.
  • The WISDOM environment facilitates the deployment of biological tools for high-throughput screening.
  • Large-scale molecular docking is feasible and efficient using distributed computing resources.