A searching method for interacting chemical compounds for target proteins using 3D structures of compound-protein complexes

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We developed the program kcombu to calculate one-to-one atomic correspondences from 2D structures of chemical compounds. The method is based on the classical concept, maximum common substructure (MCS). Our method employs the fast heuristic “build-up” algorithm, and calculates topologoically-constrained disconnected MCS (TD-MCS) in addition to conventional connected and disconnected MCS. Based on this program, we developed a template-based structural prediction method of chemical compounds. We also researched common and specific 3D features of chemical compounds, which bind to proteins of the same family.