Development of a statistical coarse grained four-body potential by using molecular surface analysis

Abstract

A four-body statistical pseudo-potential has been developed for discriminating native and non-native protein conformations by Krishnamoorthy and co-workers. Recently, Aita and Nishigaki, two of us, have applied the potential to a fast blind docking of some peptides to a target protein. In this paper, we propose a development of new four-body statistical pseudo-potentials considering the only interactions between the amino residues to be found around protein surface. Technique of solvent excluding surface area analysis was used for this development. We expect that new four-body statistical pseudo-potential can be applied to studies of the next generation antibody and peptide drug developments.