A system for identifying and evaluating a pocket of a protein includes performing a Voronoi tessellation and developing a Voronoi diagram of a surface of the protein. All alpha-spheres on the surface of the protein are identified. The alpha-spheres are filtered based on radius and remaining alpha-spheres are clustered into alpha-clusters. At least one alpha-cluster is selected for quantitative evaluation. Alpha-sphere contact atoms are determined for a plurality of interaction points of the pocket. A Delaunay triangulation of the four contact atoms of each interaction point is performed. A plurality of alpha-spaces for each interaction point are determined. An alpha-atom and an alpha-atom contact surface area (ACSA) of each interaction point is determined. The pocket is ranked, a pocket-fragment complementarity is determined, and the pocket is matched between various conformations of the proteins.