Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

ABSTRACT: Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despi

SUBMITTER: Oldziej S 

PROVIDER: S-EPMC1140449 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature