Using the unfolded state as the reference state improves the performance of statistical potentials.

ABSTRACT: Distance-dependent statistical potentials are an important class of energy functions extensively used in modeling protein structures and energetics. These potentials are obtained by statistically analyzing the proximity of atoms in all combinatorial amino-acid pairs in proteins with known structures. In model evaluation, the statistical potential is usually subtracted by the value of a reference state for better selectivity. An ideal reference state should include the general chemical properties of polypeptide chains so that only the unique factors stabilizing the native structures are retained after calibrating on reference state. However, reference states available as of this writing rarely model specific chemical constraints of peptide bonds and therefore poorly reflect the behavior of

SUBMITTER: Liu Y 

PROVIDER: S-EPMC3491692 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature