DOCK Accessories

The relationship between the main programs in the dock suite is depicted in Figure 1. These routines will be described below.

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Main programs in DOCK suite

The program sphgen identifies the active site, and other sites of interest, and generates the sphere centers that fill the site. It has been described in the original paper (Kuntz et al. J. Mol. Biol. 1982). The program grid generates the scoring grids (Shoichet et al. J. Comp. Chem. 1992 and Meng et al. J. Comp. Chem. 1992). Within the DOCK suite of programs, the program DOCK matches spheres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations (Kuntz et al. J. Mol. Biol. 1982 and Shoichet et al. J. Comp. Chem. 1992). Program DOCK also minimizes energy based scores (Meng et al. Proteins. 1993).