Beating the millisecond barrier in molecular dynamics simulations.

Abstract

Although the principles of protein folding have been elucidated by now, correct prediction of the precise mechanism of folding from a denatured state to the native state is still a huge challenge in molecular biology. The delicate balance of molecular forces acting within the protein and the solvent, and the significant entropic contribution of the protein and solvent, make such a theoretical prediction difficult. Molecular simulations using classical force fields have enabled the theoretical prediction of folding processes. Famous examples have been provided by the distributed computing project folding@home (www.folding.stanford. edu) and the D.E. Shaw Anton computer (1). These approaches use straightforward integration of the equation of motions, something that might not be the most efficient way to achieve results. In this issue of the Biophysical Journal, Du and Bolhuis (2) demonstrate that the single-replica multistate transition interface method (MS-TIS) can be used to simulate both the folding and unfolding process of the Villin headpiece, a small 35-residue model protein, very efficiently. To understand the problem of rare events and rare event processes, let us consider a simple two-state folding model

DOI: 10.1016/j.bpj.2014.11.3477

Cite this paper

@article{No2015BeatingTM, title={Beating the millisecond barrier in molecular dynamics simulations.}, author={Frank No{\'e}}, journal={Biophysical journal}, year={2015}, volume={108 2}, pages={228-9} }