Thoroughly sampling sequence space: large-scale protein design of structural ensembles.

ABSTRACT: Modeling the inherent flexibility of the protein backbone as part of computational protein design is necessary to capture the behavior of real proteins and is a prerequisite for the accurate exploration of protein sequence space. We present the results of a broad exploration of sequence space, with backbone flexibility, through a novel approach: large-scale protein design to structural ensembles. A distributed computing architecture has allowed us to generate hundreds of thousands of diverse sequences for a set of 253 naturally occurring proteins, allowing exciting insights into the nature of protein sequence space. Designing to a structural ensemble produces a much greater diversity of sequences than previous studies have reported, and homology searches using profiles derived from the des

SUBMITTER: Larson SM 

PROVIDER: S-EPMC2373757 | biostudies-literature | 2002 Dec

REPOSITORIES: biostudies-literature