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On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors

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GDECS Computational Chemistry, AstraZeneca R&D, Mölndal, Sweden, Cancer Discovery, AstraZeneca R&D, Boston, Massachusetts, and Medicinal Chemistry, AstraZeneca R&D, Mölndal, Sweden
Cite this: J. Chem. Inf. Model. 2006, 46, 1, 401–415
Publication Date (Web):December 14, 2005
https://doi.org/10.1021/ci0503255
Copyright © 2006 American Chemical Society
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    Abstract

    Four of the most well-known, commercially available docking programs, FlexX, GOLD, GLIDE, and ICM, have been examined for their ligand-docking and virtual-screening capabilities. The relative performance of the programs in reproducing the native ligand conformation from starting SMILES strings for 164 high-resolution protein−ligand complexes is presented and compared. Applying only the native scoring functions, the latest versions of these four docking programs were also used to conduct virtual screening for 12 protein targets of therapeutic interest, involving both publicly available structures and AstraZeneca in-house structures. The capability of the four programs to correctly rank-order target-specific active compounds over alternative binders and nonbinders (decoys plus randomly selected compounds) and thereby enrich a small subset of a screening library is compared. Enrichments from the virtual-screening experiments are contrasted with those obtained with alternative 3D shape-matching and 2D similarity database-search methods.

    *

     To whom correspondence should be addressed. Phone:  +46 31 7065285 (H.C.); +46 31 7065735 (T.L.) E-mail:  hongming.chen@ astrazeneca.com (H.C.); [email protected] (T.L.).

    †

     GDECS Chemical Computing, AstraZeneca R&D.

    ‡

     Cancer Discovery, AstraZeneca R&D.

    §

     Medicinal Chemistry, AstraZeneca R&D.

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