2.6.1. Sphere Matching
The rigid body orienting code is written as a direct implementation of the isomorphous subgraph matching method of Crippen and Kuhl (Kuhl, et al. J. Comput. Chem. 1984). All receptor sphere pairs and atom center pairs are considered for inclusion in a matching clique. This is more computationally demanding than the clique matching algorithm implemented in previous versions of that used a distance binning algorithm to restrict the clique search, in which pairs of spheres and atom centers were binned by distance. Only sphere pairs and center pairs that were within the same distance bin were considered as potential matches (Ewing, et al. J. Comput. Chem. 1997) .
The clique matching implementation avoids bin boundaries that prevent some receptor sphere and ligand atom pairs from matching, and, as a result, it can find good matches missed by previous versions of dock. The rigid body rotation code has also been corrected to avoid a singularity that occurred if the spheres in the match lay within the same plane.
There are two types of ligand orientation currently available:
(1) Automated Matching —Specify the number of orientations, and dock will generate matches until enough orientations passing the bump filter have been formed. Matches are formed best first, with respect to the difference in the ligand and site point internal distances.
(2) Manual Matching —Specify the distance and node parameters, and DOCK will generate all the matches which satisfy them. The number of orientations scored is equal to the total matches minus the orientations discarded by the user applied filters.
Multiple orientations may be written out for each molecule using the write_orientations parameter (see Ligand File Input/Output), otherwise only the best orientation is recorded.