Using the concept of transient complex for affinity predictions in CAPRI rounds 20-27 and beyond.

ABSTRACT: Predictions of protein-protein binders and binding affinities have traditionally focused on features pertaining to the native complexes. In developing a computational method for predicting protein-protein association rate constants, we introduced the concept of transient complex after mapping the interaction energy surface. The transient complex is located at the outer boundary of the bound-state energy well, having near-native separation and relative orientation between the subunits but not yet formed most of the short-range native interactions. We found that the width of the binding funnel and the electrostatic interaction energy of the transient complex are among the features predictive of binders and binding affinities. These ideas were very promising for the five affinity-related targ

SUBMITTER: Qin S 

PROVIDER: S-EPMC3842397 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature