A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field.

ABSTRACT: A method for optimizing potential-energy functions of proteins is proposed. The method assumes a hierarchical structure of the energy landscape, which means that the energy decreases as the number of native-like elements in a structure increases, being lowest for structures from the native family and highest for structures with no native-like element. A level of the hierarchy is defined as a family of structures with the same number of native-like elements (or degree of native likeness). Optimization of a potential-energy function is aimed at achieving such a hierarchical structure of the energy landscape by forcing appropriate free-energy gaps between hierarchy levels to place their energies in ascending order. This procedure is different from methods developed thus far, in which the ener

SUBMITTER: Liwo A 

PROVIDER: S-EPMC122298 | biostudies-literature | 2002 Feb

REPOSITORIES: biostudies-literature