Elastic Network Models are Robust to Variations in Formalism.

ABSTRACT: Understanding the functions of biomolecules requires insight not only from structures, but from dynamics as well. Often, the most interesting processes occur on time scales too slow for exploration by conventional molecular dynamics (MD) simulations. For this reason, alternative computational methods such as elastic network models (ENMs) have become increasingly popular. These simple, coarse-grained models represent molecules as beads connected by harmonic springs; the system's motions are solved analytically by normal mode analysis. In the past few years, many different formalisms for performing ENM calculations have emerged, and several have been optimized using all-atom MD simulations. In contrast to other studies, we have compared the various formalisms in a systematic, quantitative wa

SUBMITTER: Leioatts N 

PROVIDER: S-EPMC3424003 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature