Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

ABSTRACT: This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular m

SUBMITTER: Mori T 

PROVIDER: S-EPMC4877274 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature