Fine grained sampling of residue characteristics using molecular dynamics simulation.

ABSTRACT: In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone phi,psi angles with the first side-chain torsion angles (chi(1)) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found th

SUBMITTER: Joo H 

PROVIDER: S-EPMC2916028 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature