Character and evolution of protein–protein interfaces

Protein-protein interactions create the macromolecular assemblies and sequential signaling pathways essential for cell function. Their number far exceeds the number of proteins themselves and their experimental characterization, while improving, remains relatively slow. For these reasons, novel computational methods have important roles to play in understanding the physical basis of protein interactions, and in constraining the molecular basis of their specificity. This paper discusses methods based on multiple sequence alignments of protein homologues and phylogenetic trees.