Automated docking with grid-based energy evaluation

Authors

  • Elaine C. Meng,

    1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
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  • Brian K. Shoichet,

    1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
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  • Irwin D. Kuntz

    Corresponding author
    1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
    • Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
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Abstract

The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking algorithm with the evaluation of molecular mechanics interaction energies. The computational costs of evaluation are minimal because we precalculate the receptor-dependent terms in the potential function at points on a three-dimensional grid. In four test cases where the components of crystallographically determined complexes are redocked, the “force field” score correctly identifies the family of orientations closest to the experimental binding geometry. Scoring functions that consider only steric factors or only electrostatic factors are less successful. The force field function will play an important role in our efforts to search databases for potential lead compounds.

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