De novo structure prediction of globular proteins aided by sequence variation-derived contacts.

ABSTRACT: The advent of high accuracy residue-residue intra-protein contact prediction methods enabled a significant boost in the quality of de novo structure predictions. Here, we investigate the potential benefits of combining a well-established fragment-based folding algorithm--FRAGFOLD, with PSICOV, a contact prediction method which uses sparse inverse covariance estimation to identify co-varying sites in multiple sequence alignments. Using a comprehensive set of 150 diverse globular target proteins, up to 266 amino acids in length, we are able to address the effectiveness and some limitations of such approaches to globular proteins in practice. Overall we find that using fragment assembly with both statistical potentials and predicted contacts is significantly better than either statistical pot

SUBMITTER: Kosciolek T 

PROVIDER: S-EPMC3956894 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature