SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function

SSIPe is a method to calculate binding free-energy changes (ΔΔG_bind) of protein-protein interactions (PPIs) upon mutations at protein-protein interface. Starting from a PPI complex structure, SSPIe first generates multple structure and sequence alignments from non-redundant interface library (NIL) and STRING databases separately. The structural and sequence profiles are then combined with the physical energy function EvoEF to predict the impact of the mutations on PPI binding free energies. SSIPe can be used to guide the designing and engineering of protein-protein interactions with enhanced binding affinity, and/or for understanding the roles of disease-related mutations associated with protein-protein interactions.

This SSIPe package contains the source code and the NIL and STRING datasets. see https://github.com/tommyhuangthu/SSIPe for more information.