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Molecular docking is the process of posing, scoring and ranking small molecules in the binding sites of proteins.  Typically, a large database of molecules such as ZINC is screened and ranked using a docking program such as DOCK.  The top scoring compounds are reviewed in a hit picking party and then purchased and tested experimentally.  There are many good molecular docking programs.   DOCK is the implementation of molecular docking and virtual screening that we develop and use at UCSF and University of Toronto.