We apply moving root-mean-square deviation (mRMSD), which does not require a reference
structure, as a method for analyzing protein dynamics. This method can be used to calculate …

Recent single-molecule experiments have observed transition paths, ie, brief events where
molecules (particularly biomolecules) are caught in the act of surmounting activation …

Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …

Molecular dynamics simulation is a powerful method for investigating the structural stability,
dynamics, and function of biopolymers at the atomic level. In recent years, it has become …

Determining the optimal number and identity of structural clusters from an ensemble of
molecular configurations continues to be a challenge. Recent structural clustering methods …

Conformational memory in single-molecule dynamics has attracted recent attention and, in
particular, has been invoked as a possible explanation of some of the intriguing properties of …

Recent single-molecule experiments probed transition paths of biomolecular folding and, in
particular, measured the time biomolecules spend while crossing their free energy barriers …

Chemists visualize chemical reactions as motion along one-dimensional “reaction
coordinates” over free energy barriers. Various rate theories, such as transition state theory …

Transition paths are brief excursions taken by molecules when they cross barriers
separating stable molecular conformations. When observed in single-molecule experiments …

Conformational sampling of biomolecules using molecular dynamics simulations often
produces a large amount of high dimensional data that makes it difficult to interpret using …