title: Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent.
abstract: 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 MD simulations of the folding of an α and a β 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.
authors: European Centre for Theoretical Nuclear Physics and Related Areas (ECT*-FBK), Strada delle Tabarelle 287, Villazzano (Trento) 38123, Italy.|Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo (Trento) 38123, Italy.
authors: S
authors: S
authors: A Beccara
authors: Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) 38123, Italy.
authors: L
authors: L
authors: Fant
authors: Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14, Povo (Trento) 38123, Italy.|Trento Institute for Fundamental Physics and Applications (INFN-TIFPA), Via Sommarive 14, Povo (Trento) 38123, Italy.
authors: P
authors: P
authors: Faccioli
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008840:Microfilament Proteins / Q000737:chemistry*; D008956:Models, Chemical; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: D008840:Microfilament Proteins; C026615:villin