Comparison of Rosetta flexible-backbone computational protein design methods on binding interactions.

ABSTRACT: Computational design of binding sites in proteins remains difficult, in part due to limitations in our current ability to sample backbone conformations that enable precise and accurate geometric positioning of side chains during sequence design. Here we present a benchmark framework for comparison between flexible-backbone design methods applied to binding interactions. We quantify the ability of different flexible backbone design methods in the widely used protein design software Rosetta to recapitulate observed protein sequence profiles assumed to represent functional protein/protein and protein/small molecule binding interactions. The CoupledMoves method, which combines backbone flexibility and sequence exploration into a single acceptance step during the sampling trajectory, better rec

SUBMITTER: Loshbaugh AL 

PROVIDER: S-EPMC6901717 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature