Motif-directed flexible backbone design of functional interactions.

ABSTRACT: Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse-grained sampling of possible side-chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side-chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side-chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movemen

SUBMITTER: Havranek JJ 

PROVIDER: S-EPMC2774439 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature