| Abstract
| - The performance of several commercially available docking programs is compared in the contextof 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 MDLdrug data report and 49 known ligands. For many of the known ligands, crystal structures ofthe relevant protein−ligand complexes were available. We attempted to run experiments witheach docking method that were as similar as possible. For a given docking method, hit rateswere 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 resembleknown crystal structures is both method- and target-dependent.
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