A Novel Method to Determine the Assembling Space between Two Protein Subunits

It is thought that proteins recognize their partners by complementarity. The parameters for the charge complementarity and many analyses have been reported not only in small ligand to protein interactions but also protein-protein interactions. However, there have been few reports about shape complementarity, especially for the protein-protein interfaces. The SC program [1] may be the only method available to describe shape complementarity previously reported. However, this method is based on the surface shape. To assess the shape complementarity, we propose to calculate the volume between two protein subunits and thereby facilitate estimation of shape complementarity independently of the surface shape.