Structural Descriptors of Protein-Protein Binding Sites

Structural bioinformatics provides new tools for investigating protein-protein interactions at the molecular level. We present two types of structural descriptors for efficiently representing and comparing protein-protein binding sites and surface patches. The descriptors are based on distributions of distances between five types of functional atoms, thereby capturing the spatial arrangement of physicochemical properties in 3D space. Experiments with the method are performed on two tasks: (1) detection of binding sites with known similarity from homologous proteins, and (2) scanning of the surfaces of two non-homologous proteins for similar regions.