DOCK addresses the problem of "docking" molecules to each other. It explores ways in which two molecules, such as a drug and an enzyme or protein receptor, might fit together. Compounds which dock to each other well, like pieces of a three-dimensional jigsaw puzzle, have the potential to bind. So, why is it important to able to identify small molecules which may bind to a target macromolecule? A compound which binds to a biological macromolecule may inhibit its function, and thus act as a drug.
DOCK generates many possible orientations (and more recently, conformations) of a putative ligand within a user-selected region of a receptor structure. These orientations may be scored using several schemes designed to measure steric and/or chemical complementarity of the receptor-ligand complex. These scores may be used to evaluate likely orientations of a single ligand, or to rank molecules from a database.
More information about the algorithms used in DOCK 3.5 and DOCK 4.0 may be found by selecting the links listed in the blue area to your left.
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October 2000 DOCK User Group Meeting information.