A versatile method for systematic conformational searches: application to CheY.

ABSTRACT: A novel molecular structure prediction method, the Z Method, is described. It provides a versatile platform for the development and use of systematic, grid-based conformational search protocols, in which statistical information (i.e., rotamers) can also be included. The Z Method generates trial structures by applying many changes of the same type to a single starting structure, thereby sampling the conformation space in an unbiased way. The method, implemented in the CHARMM program as the Z Module, is applied here to an illustrative model problem in which rigid, systematic searches are performed in a 36-dimensional conformational space that describes the relative positions of the 10 secondary structural elements of the protein CheY. A polar hydrogen representation with an implicit solvatio

SUBMITTER: Petrella RJ 

PROVIDER: S-EPMC3298744 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature