Mimicking the folding pathway to improve homology-free protein structure prediction.

ABSTRACT: Since the demonstration that the sequence of a protein encodes its structure, the prediction of structure from sequence remains an outstanding problem that impacts numerous scientific disciplines, including many genome projects. By iteratively fixing secondary structure assignments of residues during Monte Carlo simulations of folding, our coarse-grained model without information concerning homology or explicit side chains can outperform current homology-based secondary structure prediction methods for many proteins. The computationally rapid algorithm using only single (phi,psi) dihedral angle moves also generates tertiary structures of accuracy comparable with existing all-atom methods for many small proteins, particularly those with low homology. Hence, given appropriate search strategi

SUBMITTER: DeBartolo J 

PROVIDER: S-EPMC2656149 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature