A force field for virtual atom molecular mechanics of proteins.

ABSTRACT: Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of C alpha atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find

SUBMITTER: Korkut A 

PROVIDER: S-EPMC2734882 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature