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Comparison of Topological, Shape, and Docking Methods in Virtual Screening
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Section: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.
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This article has been cited by 36 ACS Journal articles (5 most recent appear below).
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Xiaofeng Liu, Hualiang Jiang, and Honglin LiJournal of Chemical Information and Modeling2011 51 (9), 2372-2385We developed a novel approach called SHAFTS (SHApe-FeaTure Similarity) for 3D molecular similarity calculation and ligand-based virtual screening. SHAFTS adopts a hybrid similarity metric combined with molecular shape and colored (labeled) chemistry ...
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- Published In Issue July 23, 2007
- Received February 7, 2007
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