A Combinatorial Shape Matching Algorithm for Rigid Protein Docking

Abstract

AbstractThe protein docking problem is to predict the structure of protein-protein complexes from the structures of individual proteins. It is believed that shape complementarity plays a dominant role in protein docking. Recently, it has been shown empirically by Bespamaytnikh et al [4] that the shape complementarity (measured by a score function) is sufficient for the bound protein docking problem, in which proteins are taken directly from the known protein-protein complex and reassembled, treating each protein as a rigid body. In this paper, we study the shape complementarity measured by their score function from a theoretical point of view. We give a combinatorial characterization of the docked configuration achieved by the maximum score. This leads to a simple polynomial time algorithm to find such a configuration. The arrangement of spheres inspired by the combinatorial characterization plays an essential role in an efficient local search heuristic of Choi et al [7] for rigid protein docking. We also show that our general idea can be used to give simple algorithms for some point pattern matching problems in any dimension.KeywordsBipartite GraphScore FunctionRigid MotionProtein DockingLocal Search HeuristicThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.