Discovering Protein-Protein Interaction Sites from Sequence and Structure

This chapter gives a comprehensive introduction of the sequence/structural features that are characteristic of protein-protein interaction sites and reviews state-of-the-art methodologies for protein-protein binding site prediction. Protein-protein interaction residues are largely responsible for mediating physical binding processes such as inhibitory effects through enzyme-inhibitor interaction, initiating immune response by an antibody-antigen interaction, and regulation of cell signaling proteins. Currently, various methods are available for predicting protein-protein interaction sites, which allow a residue-level understanding of the physical protein binding phenomena presented by the global construction protein-protein interaction networks. The overview of the discussed protein-protein binding site prediction strategies and detailed comparison of their weaknesses and strengths is aimed towards assisting protein researchers in gaining more insight to protein-protein interaction networks.