Finding biologically relevant protein domain interactions: conserved binding mode analysis.

ABSTRACT: Proteins evolved through the shuffling of functional domains, and therefore, the same domain can be found in different proteins and species. Interactions between such conserved domains often involve specific, well-determined binding surfaces reflecting their important biological role in a cell. To find biologically relevant interactions we developed a method of systematically comparing and classifying protein domain interactions from the structural data. As a result, a set of conserved binding modes (CBMs) was created using the atomic detail of structure alignment data and the protein domain classification of the Conserved Domain Database. A conserved binding mode is inferred when different members of interacting domain families dock in the same way, such that their structural complexes su

SUBMITTER: Shoemaker BA 

PROVIDER: S-EPMC1855242 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature