Design of an optimal Chebyshev-expanded discrimination function for globular proteins.

ABSTRACT: We describe the construction of a scoring function designed to model the free energy of protein folding. An optimization technique is used to determine the best functional forms of the hydrophobic, residue-residue and hydrogen-bonding components of the potential. The scoring function is expanded by use of Chebyshev polynomials, the coefficients of which are determined by minimizing the score, in units of standard deviation, of native structures in the ensembles of alternate decoy conformations. The derived effective potential is then tested on decoy sets used conventionally in such studies. Using our scoring function, we achieve a high level of discrimination between correct and incorrect folds. In addition, our method is able to represent functions of arbitrary shape with fewer parameters

SUBMITTER: Fain B 

PROVIDER: S-EPMC2373672 | biostudies-literature | 2002 Aug

REPOSITORIES: biostudies-literature