Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm

F Marini; C Camilloni; D Provasi; R A Broglia; G Tiana

doi:10.1016/j.gene.2008.06.003

Metadynamic sampling of the free-energy landscapes of proteins coupled with a Monte Carlo algorithm

Gene. 2008 Oct 1;422(1-2):37-40. doi: 10.1016/j.gene.2008.06.003. Epub 2008 Jun 6.

Authors

F Marini¹, C Camilloni, D Provasi, R A Broglia, G Tiana

Affiliation

¹ Department of Physics, University of Milan, via Celoria 16, 20133 Milan, Italy. franz.marini@mi.infn.it

PMID: 18593595
DOI: 10.1016/j.gene.2008.06.003

Abstract

Metadynamics is a powerful computational tool to obtain the free-energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus to gain an ever-increasing understanding on the general principles underlying the mechanism of protein folding. We show that it is possible to couple metadynamics and Monte Carlo algorithms to obtain the free energy of model proteins in a way which is computationally very economical.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Models, Molecular*
Monte Carlo Method*
Proteins / chemistry*
Proteins / genetics
Surface Properties
Thermodynamics

Substances

Proteins