Data Mining in Protein Binding Cavities

The molecular function of a protein is coupled to the binding of a substrate or an endogenous ligand to a well defined binding cavity. To detect functional relationships among proteins, their binding-site exposed physicochemical characteristics were described by assigning generic pseudocenters to the functional groups of the amino acids flanking a particular active site. These pseudocenters were assembled into small substructures and their spatial similarity with appropriate chemical properties was examined. If two substructures of two binding cavities are found to be similar, they form the basis for an expanded comparison of the complete cavities. Preliminary tests indicate the benefit of this method and motivate further studies.