Virtual ligand screening uses computation to discover new ligands of a protein by screening one or more of its structural models against a database of potential ligands. Comparative protein structure modeling extends the applicability of virtual screening beyond the atomic structures determined by X-ray crystallography or NMR spectroscopy. We will describe an integrated modeling and docking protocol, combining comparative modeling by MODELLER and virtual ligand screening by DOCK. The presentation will include a description of a statistical scoring function for ligand screening as well as several applications to specific proteins of interest to the Enzyme Function Initiative (http://enzymefunction.org/) and Pharmacogenetics of Membrane Transporters consortium (http://pharmacogenetics.ucsf.edu/).
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