Predicting protein–protein interactions in the context of protein evolution

TLDR: The evolutionary assumptions implicit in many of the protein interaction prediction methods are elucidated and the caution needed in deploying certain evolutionary assumptions is drawn, in particular cross-organism transfer of interactions by sequence homology.

Abstract: Here we review the methods for the prediction of protein interactions and the ideas in protein evolution that relate to them. The evolutionary assumptions implicit in many of the protein interaction prediction methods are elucidated. We draw attention to the caution needed in deploying certain evolutionary assumptions, in particular cross-organism transfer of interactions by sequence homology, and discuss the known issues in deriving interaction predictions from evidence of co-evolution. We also conject that there is evolutionary knowledge yet to be exploited in the prediction of interactions, in particular the heterogeneity of interactions, the increasing availability of interaction data from multiple species, and the models of protein interaction network growth.