Fast Geometric Algorithm for Rigid Protein Docking

Y. Wang, P. K. Agarwal, P. Brown , H. Edelsbrunner and J. RudolphDuke University, Durham, North CarolinaAbstract. In this paper, we present an efficient algorithm to generate a reasonably small butreliable set of coarse protein docking configurations by aligning meaningful features on proteinsurfaces. A protein is considered as a rigid body in our approach, and the output producedcan serve as input data for other local improvement methods that allow protein flexibility. Wedemonstrate the performance of our algorithm by testing our algorithm on a diverse set ofprotein complexes from the Protein Data Bank.

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