The roles of entropy and kinetics in structure prediction.

ABSTRACT:

Background

Here we continue our efforts to use methods developed in the folding mechanism community to both better understand and improve structure prediction. Our previous work demonstrated that Rosetta's coarse-grained potentials may actually impede accurate structure prediction at full-atom resolution. Based on this work we postulated that it may be time to work completely at full-atom resolution but that doing so may require more careful attention to the kinetics of convergence.

Methodology/principal findings

To explore the possibility of working entirely at full-atom resolution, we apply enhanced sampling algorithms and the free energy theory developed in the folding mechanism community to full-atom protein structure prediction with the prominent Rosetta package. We fin

SUBMITTER: Bowman GR 

PROVIDER: S-EPMC2688754 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature