Comparison of Automated Docking Programs as Virtual Screening Tools

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.