A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.

ABSTRACT: In this article, we present an enhanced sampling method based on a hybrid Hamiltonian which combines experimental distance restraints with a bias dependent from multiple path-dependent variables. This simulation method determines the bias-coordinates on the fly and does not require a priori knowledge about reaction coordinates. The hybrid Hamiltonian accelerates the sampling of proteins, and, combined with experimental distance information, the technique considers the restraints adaptively and in dependency of the system's intrinsic dynamics. We validate the methodology on the dipole relaxation of two water models and the conformational landscape of dialanine. Using experimental NMR-restraint data, we explore the folding landscape of the TrpCage mini-protein and in a second e

SUBMITTER: Peter EK 

PROVIDER: S-EPMC6359555 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature