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

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ADVERTISEMENT Journal of Medicinal ChemistryVol 47/Issue 7Article Cite Share Jump to Expand ARTICLEFebruary 27, 2004 Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking AccuracyClick to copy article link Richard A. FriesnerJay L. BanksRobert B. MurphyThomas A. HalgrenJasna J. KlicicDaniel T. MainzMatthew P. RepaskyEric H. KnollMee ShelleyJason K. PerryDavid E. ShawPerry FrancisPeter S. Shenkin View Author Information View Author Information Loading Institutional Login Options… Other Access Options Supporting Information (1) Abstract

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.

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To whom correspondence should be addressed. Phone: 212-854-7606. Fax: 212-854-7454. E-mail: rich@chem.columbia.edu.

†

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.

Supporting Information Available

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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Analytical Chemistry 2025, 97 (37) , 20228-20236. https://doi.org/10.1021/acs.analchem.5c03103 Load more citations Get e-Alerts Journal of Medicinal Chemistry Cite this: J. Med. Chem. 2004, 47, 7, 1739–1749 https://doi.org/10.1021/jm0306430 Published February 27, 2004 Copyright © 2004 American Chemical Society Request reuse permissions Article Views 42k Citations 8515 Learn about these metrics Recommended Articles