Algorithm for backrub motions in protein design.

ABSTRACT:

Motivation

The Backrub is a small but kinematically efficient side-chain-coupled local backbone motion frequently observed in atomic-resolution crystal structures of proteins. A backrub shifts the C(alpha)-C(beta) orientation of a given side-chain by rigid-body dipeptide rotation plus smaller individual rotations of the two peptides, with virtually no change in the rest of the protein. Backrubs can therefore provide a biophysically realistic model of local backbone flexibility for structure-based protein design. Previously, however, backrub motions were applied via manual interactive model-building, so their incorporation into a protein design algorithm (a simultaneous search over mutation and backbone/side-chain conformation space) was infeasible.

Results

We present a combi

SUBMITTER: Georgiev I 

PROVIDER: S-EPMC2718647 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature