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Molecular docking is the process of posing, scoring and ranking small molecules in the binding sites of proteins to prioritize compounds for aquisition and experimental testing. Typically, a large database of small molecules such as ZINC is screened 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 molecular docking programs to choose from (see below). DOCK 3 is the implementation of molecular docking and virtual screening that we develop and use at UCSF.

The goal of molecular docking screens is often ligand discovery - new chemical matter than can be optimized using medicinal chemistry techniques. Another approach to ligand discovery is to simply use cheminformatics methods such as ZINC to identify purchasable compounds.

Docking Programs

There are many docking programs. All of them have been successfully used for ligand discovery. The first three are from UCSF.

If we have forgotten your program, please add it here.

The difference between the Docking category and the Category:DOCK category is that DOCK is specific to our software, whereas Docking (this page) includes all docking programs and the approach in general.