A new probability method to understand protein-protein interface formation mechanism at amino acid level

Protein-protein interactions and recognitions are essential for organisms to accomplish many cellular processes. The interface compositions of protein-protein complexes are the key to understand the molecular mechanisms of these processes. There are many studies on near native interface recognition for protein-protein interactions, but the formation mechanism of protein-protein interface is still ambiguous. Here, we propose a new probability method to understand protein-protein interface formation mechanism at amino acid level. The probability of two surface residues from two monomers as a true interface residue pair is estimated by their properties in the structures of protein monomers. Estimated residue pairs with interface possibilities combine together to form a protein-protein interface. The possibility values are integrated to discriminate the near native interface from non-near native ones. In this paper, five simple probability based methods are constructed for near native interface recognition based on several geometric and physicochemical descriptors. The performances are comparable to the best results reported previously, which suggests this is a promising way. The idea proposed here will have a certain significance to the future research on protein-protein interactions.