Lessons from the design of a novel atomic potential for protein folding.

ABSTRACT: We investigate all-atom potentials of mean force for estimating free energies in protein folding and fold recognition. We search through the space potentials and design novel atomic potentials with a random mixing approximation and a contact-correlated Gaussian approximation of decoy states. We show that the two derived potentials are highly correlated, supporting the use of the random energy model as an accurate statistical description of protein conformational states. The novel atomic potentials perform well in a Z-score and fold decoy recognition test. Furthermore, the designed atomic potential performs slightly and significantly better than atomic potentials derived under a quasi-chemical assumption. While accounting for connectivity correlations between atom types does not improve the

SUBMITTER: Chen WW 

PROVIDER: S-EPMC2253347 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature