Protein model refinement using an optimized physics-based all-atom force field.

ABSTRACT: One of the greatest challenges in protein structure prediction is the refinement of low-resolution predicted models to high-resolution structures that are close to the native state. Although contemporary structure prediction methods can assemble the correct topology for a large fraction of protein domains, such approximate models are often not of the resolution required for many important applications, including studies of reaction mechanisms and virtual ligand screening. Thus, the development of a method that could bring those structures closer to the native state is of great importance. We recently optimized the relative weights of the components of the Amber ff03 potential on a large set of decoy structures to create a funnel-shaped energy landscape with the native structure at the glob

SUBMITTER: Jagielska A 

PROVIDER: S-EPMC2448826 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature