Abstract

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.

Keywords

Virtual screeningDocking (animal)DecoyBenchmarkingComputer scienceChemical similarityComputational biologyArtificial intelligenceMetric (unit)Data miningLigand (biochemistry)ChemistryBioinformaticsBiologyStructural similarityEngineeringDrug discoveryMedicineBiochemistry

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Publication Info

Year
2007
Type
article
Volume
47
Issue
4
Pages
1504-1519
Citations
414
Access
Closed

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Georgia B. McGaughey, Robert P. Sheridan, Christopher I. Bayly et al. (2007). Comparison of Topological, Shape, and Docking Methods in Virtual Screening. Journal of Chemical Information and Modeling , 47 (4) , 1504-1519. https://doi.org/10.1021/ci700052x

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DOI
10.1021/ci700052x