A Pareto-optimal refinement method for protein design scaffolds.

ABSTRACT: Computational design of protein function involves a search for amino acids with the lowest energy subject to a set of constraints specifying function. In many cases a set of natural protein backbone structures, or "scaffolds", are searched to find regions where functional sites (an enzyme active site, ligand binding pocket, protein-protein interaction region, etc.) can be placed, and the identities of the surrounding amino acids are optimized to satisfy functional constraints. Input native protein structures almost invariably have regions that score very poorly with the design force field, and any design based on these unmodified structures may result in mutations away from the native sequence solely as a result of the energetic strain. Because the input structure is already a stable prote

SUBMITTER: Nivon LG 

PROVIDER: S-EPMC3614904 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature