Self Consistent Path Sampling: Making Accurate All-Atom Protein Folding Simulations Possible on Small Computer Clusters

Autor:	Orioli, S., Beccara, S. A, Faccioli, P.
Rok vydání:	2017
Předmět:	Physics - Biological Physics Condensed Matter - Soft Condensed Matter Quantitative Biology - Biomolecules
Druh dokumentu:	Working Paper
Popis:	We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble of reactive pathways, exponentially reducing the cost of simulating thermally activated transitions. The algorithm also yields a rigorous stochastic estimate of the reaction coordinate. After illustrating this approach on a simple toy model, we successfully validate it against the results of ultra-long plain MD protein folding simulations for a fast folding protein (Fip35), which were performed on the Anton supercomputer. Using our algorithm, computing a folding trajectory for this protein requires only 1000 core hours, a computational load which could be even carried out on a desktop workstation. Comment: 10 pages, 7 figures
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/1705.02180 Zobrazit plný text záznamu View this record from Arxiv