Coarse-grained models reveal functional dynamics--II. Molecular dynamics simulation at the coarse-grained level--theories and biological applications.

ABSTRACT: Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the absence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faste

SUBMITTER: Chng CP 

PROVIDER: S-EPMC2735960 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature