The protein docking problem refers to the task of predicting the appropriate matching of one protein molecule (the receptor) to another (the ligand), when attempting to bind them to form a stable complex. Research shows that matching the three-dimensional geometric structures of proteins plays a key role in determining a so-called docking pair. However, the active sites which are responsible for the binding do not always present a rigid-body shape matching problem. Rather, they may undergo deformations when docking occurs, which complicates the process. To address this issue, we present an isometry-invariant and topologically robust partial shape descriptor method for finding complementary protein sites. Our method employs Heat Kernel Signature shape descriptors which are based on the diffusion of heat on surfaces. Our experimental results against the ProteinProtein Benchmark 4.0 demonstrate the viability of our approach.
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