Computational design of protein-protein interactions

Abstract

Computational protein design strategies have been developed to reengineer protein-protein interfaces in an automated, generalizable fashion. In the past two years, these methods have been successfully applied to generate chimeric proteins and protein pairs with specificities different from naturally occurring protein-protein interactions. Although there are shortcomings in current approaches, both in the way conformational space is sampled and in the energy functions used to evaluate designed conformations, the successes suggest we are now entering an era in which computational methods can be used to modulate, reengineer and design protein-protein interaction networks in living cells.