Journal of Computer-Aided Molecular Design

, Volume 10, Issue 4, pp 293–304 | Cite as

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

  • Garrett M. Morris
  • David S. Goodsell
  • Ruth Huey
  • Arthur J. Olson
Research Papers

Summary

AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.

Keywords

Inhibitor Receptor Simulated annealing Drug design 

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Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • Garrett M. Morris
    • 1
  • David S. Goodsell
    • 1
  • Ruth Huey
    • 1
  • Arthur J. Olson
    • 1
  1. 1.Department of Molecular Biology, MB-5The Scripps Research InstituteLa JollaU.S.A.

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