Abstract

The performance of several commercially available docking programs is compared in the context of virtual screening. Five different protein targets are used, each with several known ligands. The simulated screening deck comprised 1000 molecules from a cleansed version of the MDL drug data report and 49 known ligands. For many of the known ligands, crystal structures of the relevant protein-ligand complexes were available. We attempted to run experiments with each docking method that were as similar as possible. For a given docking method, hit rates were improved versus what would be expected for random selection for most protein targets. However, the ability to prioritize known ligands on the basis of docking poses that resemble known crystal structures is both method- and target-dependent.

Keywords

Docking (animal)Virtual screeningProtein–ligand dockingChemistryComputational biologyDrug discoveryBiochemistry

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Year
2005
Type
article
Volume
48
Issue
4
Pages
962-976
Citations
205
Access
Closed

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Maxwell D. Cummings, Renée L. DesJarlais, Alan C. Gibbs et al. (2005). Comparison of Automated Docking Programs as Virtual Screening Tools. Journal of Medicinal Chemistry , 48 (4) , 962-976. https://doi.org/10.1021/jm049798d

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DOI
10.1021/jm049798d