Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions.

ABSTRACT: Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard-Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain co

SUBMITTER: Gaines JC 

PROVIDER: S-EPMC7263838 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature