A Patch-by-Patch Shape Matching Procedure for Rigid Body Docking

Docking simulates molecular interactions. Protein protein docking, owing to the sizes of molecules, is a very challenging problem. As the number of degrees of freedom in the molecular structure of proteins is huge, docking algorithms consider the molecules as relatively rigid bodies. Shape matching of two protein molecules is computationally difficult because the possibilities of matching the molecules grow exponentially with the size of molecules which gives a large search space. A new scheme is proposed in this paper for shape matching in rigid body docking. The scheme models the molecular surface as a network of locally characterized surface patches connected to each other at their boundaries. For shape matching of molecules, a patch-by-patch shape matching strategy is used. The procedure suggested for shape matching can be easily included in an optimization routine for finding the best binding conformations of two protein molecules.