Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …

Markov state models (MSMs) based on molecular dynamics (MD) simulations are routinely
employed to study protein folding, however, their application to functional conformational …

The function of complex biomolecular machines relies heavily on their conformational
changes. Investigating these functional conformational changes is therefore essential for …

Molecular dynamics simulations are a powerful means of understanding conformational
changes. However, it is still difficult to simulate biologically relevant time scales without the …

Under normal cellular conditions, the tumor suppressor protein p53 is kept at low levels in
part due to ubiquitination by MDM2, a process initiated by binding of MDM2 to the …

Interest in atomically detailed simulations has grown significantly with recent advances in
computational hardware and Markov state modeling (MSM) methods, yet outstanding …

In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM)
methodologies have made possible accurate and efficient estimation of kinetic rates and …

There is increasing evidence that protein dynamics and conformational changes can play an
important role in modulating biological function. As a result, experimental and computational …

Computational modeling of assembly is challenging for many systems, because their
timescales can vastly exceed those accessible to simulations. This article describes the …