Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

ABSTRACT: Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain move

SUBMITTER: Smith CA 

PROVIDER: S-EPMC3138746 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature