The many faces of protein-protein interactions: A compendium of interface geometry.

ABSTRACT: A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding

SUBMITTER: Kim WK 

PROVIDER: S-EPMC1584320 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature