Predictive energy landscapes for protein-protein association.

ABSTRACT: We investigate protein-protein association using the associative-memory, water-mediated, structure, and energy model (AWSEM), a coarse-grained protein folding model that has been optimized using energy-landscape theory. The potential was originally parameterized by enforcing a funneled nature for a database of dimeric interfaces but was later further optimized to create funneled folding landscapes for individual monomeric proteins. The ability of the model to predict interfaces was not tested previously. The present results show that simulated annealing of the model indeed is able to predict successfully the native interfaces of eight homodimers and four heterodimers, thus amounting to a flexible docking algorithm. We go on to address the relative importance of monomer geometry, flexibilit

SUBMITTER: Zheng W 

PROVIDER: S-EPMC3511104 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature