For the automatic detection and comparison of putative binding cavities the Cavbase system has been developed which uses a coarse-grained set of pseudocenters to represent the physicochemical properties of a binding site and employs a graph-based procedure to calculate similarities between two binding sites.  In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. 
Cavbase
In a recent work, we proposed the method Local Cliques (LC) for the efficient comparison of Cavbase binding sites. 
Local Cliques (LC)
Acceleration of Binding Site Comparisons by Graph Partitioning.The comparison of protein binding sites is a prominent task in computational chemistry and has been studied in many different ways. 
Graph Partitioning