Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale.

ABSTRACT: Cellular functions are performed through protein-protein interactions; therefore, identification of these interactions is crucial for understanding biological processes. Recent studies suggest that knowledge-based approaches are more useful than "blind" docking for modeling at large scales. However, a caveat of knowledge-based approaches is that they treat molecules as rigid structures. The Protein Data Bank (PDB) offers a wealth of conformations. Here, we exploited an ensemble of the conformations in predictions by a knowledge-based method, PRISM. We tested "difficult" cases in a docking-benchmark data set, where the unbound and bound protein forms are structurally different. Considering alternative conformations for each protein, the percentage of successfully predicted interactions incr

SUBMITTER: Kuzu G 

PROVIDER: S-EPMC3685852 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature