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 …

The “protein folding problem” consists of three closely related puzzles:(a) What is the folding
code?(b) What is the folding mechanism?(c) Can we predict the native structure of a protein …

Markov state models of molecular kinetics (MSMs), in which the long-time statistical
dynamics of a molecule is approximated by a Markov chain on a discrete partition of …

We present the latest version of the Groningen Molecular Simulation program package,
GROMOS05. It has been developed for the dynamical modelling of (bio) molecules using …

To meet the challenge of modeling the conformational dynamics of biological
macromolecules over long time scales, much recent effort has been devoted to constructing …

Markov state models (MSMs) have proven valuable in studying the dynamics of protein
conformational changes via statistical analysis of molecular dynamics simulations. In MSMs …

A rigorous formalism for the extraction of state-to-state transition functions from a Boltzmann-
weighted ensemble of microcanonical molecular dynamics simulations has been developed …

We construct coarse master equations for peptide folding dynamics from atomistic molecular
dynamics simulations. A maximum-likelihood propagator-based method allows us to extract …

Proteins are the molecular machines of life. The multitude of possible conformations that
proteins can adopt determines their free-energy landscapes. However, the inherently high …

The kinetics and thermodynamics of complex transitions in biomolecules can be modeled in
terms of a network of transitions between the relevant conformational substates. Such a …