Study of a highly accurate and fast protein–ligand docking method based on molecular dynamics: Research Articles

  • Authors:

  • M. Taufer;M. Crowley;D. J. Price;A. A. Chien;C. L. Brooks, III

  • Affiliations:

  • Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.;Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.;Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.;Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.;Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, U.S.A.

  • Venue:
  • Concurrency and Computation: Practice & Experience - Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004)
  • Year:
  • 2005

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Abstract

Few methods use molecular dynamics simulations in concert with atomically detailed force fields to perform protein–ligand docking calculations because they are considered too time demanding, despite their accuracy. In this paper we present a docking algorithm based on molecular dynamics which has a highly flexible computational granularity. We compare the accuracy and the time required with well-known, commonly used docking methods such as AutoDock, DOCK, FlexX, ICM, and GOLD. We show that our algorithm is accurate, fast and, because of its flexibility, applicable even to loosely coupled distributed systems such as desktop Grids for docking. Copyright © 2005 John Wiley & Sons, Ltd.