Comparison of Topological, Shape, and Docking Methods in Virtual Screening

Virtual screening benchmarking studies were carried out on 11 targets to evaluate the performance of three commonly used approaches: 2D ligand similarity (Daylight, TOPOSIM), 3D ligand similarity (SQW, ROCS), and protein structure-based docking (FLOG, FRED, Glide). Active and decoy compound sets we...

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Bibliographic Details
Published in:	Journal of chemical information and modeling 2007-07, Vol.47 (4), p.1504-1519
Main Authors:	McGaughey, Georgia B, Sheridan, Robert P, Bayly, Christopher I, Culberson, J. Chris, Kreatsoulas, Constantine, Lindsley, Stacey, Maiorov, Vladimir, Truchon, Jean-Francois, Cornell, Wendy D
Format:	Article
Language:	eng
Subjects:	Binding Sites Chemistry Chemistry, Pharmaceutical Comparative analysis Ligands Methods Molecular Structure Molecules
Online Access:	Get full text
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Summary:	Virtual screening benchmarking studies were carried out on 11 targets to evaluate the performance of three commonly used approaches: 2D ligand similarity (Daylight, TOPOSIM), 3D ligand similarity (SQW, ROCS), and protein structure-based docking (FLOG, FRED, Glide). Active and decoy compound sets were assembled from both the MDDR and the Merck compound databases. Averaged over multiple targets, ligand-based methods outperformed docking algorithms. This was true for 3D ligand-based methods only when chemical typing was included. Using mean enrichment factor as a performance metric, Glide appears to be the best docking method among the three with FRED a close second. Results for all virtual screening methods are database dependent and can vary greatly for particular targets.
ISSN:	1549-9596 1549-960X