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BDOCK: Integrating the degree of burial of surface residues into protein-protein docking

The binding sites of enzyme-inhibitor complexes always involve a very deep buried pocket. It is also believed that the binding sites are more conserved than the rest of surface. Based on this knowledge, we develop a system called BDOCK, which uses both the degree o f burial and conservation to improve docking. Frist, we propose a novel shape complementary scoring function for the initial docking stage, which takes the degree of burial of surface residues into account as different weights.. The alogrithm of BDOCK is illustrated in the following figure. The numbers represent the buried degrees of surface residues.

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