A free-rotating and self-avoiding chain model for deriving statistical potentials based on protein structures.

ABSTRACT: Statistical potentials have been widely used in protein studies despite the much-debated theoretical basis. In this work, we have applied two physical reference states for deriving the statistical potentials based on protein structure features to achieve zero interaction and orthogonalization. The free-rotating chain-based potential applies a local free-rotating chain reference state, which could theoretically be described by the Gaussian distribution. The self-avoiding chain-based potential applies a reference state derived from a database of artificial self-avoiding backbones generated by Monte Carlo simulation. These physical reference states are independent of known protein structures and are based solely on the analytical formulation or simulation method. The new potentials performed

SUBMITTER: Cheng J 

PROVIDER: S-EPMC1868969 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature