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Glide:  A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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Department of Chemistry, Columbia University, New York, New York 10036, Schrödinger, L.L.C., 120 W. 45th Street, New York, New York 10036, Schrödinger, L.L.C., 1500 SW First Avenue, Portland, Oregon 97201, and D. E. Shaw Research and Development, 120 W. 45th Street, New York, New York 10036
Cite this: J. Med. Chem. 2004, 47, 7, 1739–1749
Publication Date (Web):February 27, 2004
https://doi.org/10.1021/jm0306430
Copyright © 2004 American Chemical Society
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    Abstract

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    Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.

    *

     To whom correspondence should be addressed. Phone:  212-854-7606. Fax:  212-854-7454. E-mail:  [email protected].

    †

     Columbia University.

    ‡

     Schrödinger, L.L.C., NY.

    ‖

     Present address:  Serono International, S.A, CH-1211 Geneva 20, Switzerland.

    §

     Schrödinger, L.L.C., OR.

    #

     Schrödinger, L.L.C., NY and D. E. Shaw Research and Development.

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    Table S1, listing detailed results for docking ligands from 282 cocrystallized complexes into the protein sites with Glide 2.5. This material is available free of charge via the Internet at http://pubs.acs.org.

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