Understanding Protein-Protein Interface Formation Mechanism in a New Probability Way at Amino Acid Level.

Although many studies about near native protein-protein interface recognition have been done in the past thirty years, the formation mechanism of protein-protein interface is still ambiguous. Here, we propose a new probability way to understand protein-protein interface formation mechanism at amino acid level. The probability of two surface residues from different monomers as a true interface residue pair in the complex is estimated by their geometric and physicochemical properties in the structures of protein monomers. The residue pairs with different probabilities combine together to form a protein-protein interface. The probabilities of residue pairs on candidate interfaces are integrated for near native interface recognition. Five simple probability based discriminants are constructed based on the distances and contact areas between residues. The performances are comparable to the ones of the sophisticated methods developed previously. The idea proposed in this work will make positive influence on the future study of protein-protein interactions.