Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent

Autor:	Beccara, S. a, Fant, L., Faccioli, P.
Rok vydání:	2014
Předmět:	Condensed Matter - Soft Condensed Matter Quantitative Biology - Biomolecules
Druh dokumentu:	Working Paper
Popis:	We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller. Comment: Accepted for publication on Phys. Rev. Lett
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/1405.6104 Zobrazit plný text záznamu View this record from Arxiv