Experimental studies of protein folding are hampered by the fact that only low-resolution
structural data can be obtained with sufficient temporal resolution. Molecular dynamics …

A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …

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 …

Fast-folding proteins have been a major focus of computational and experimental study
because they are accessible to both techniques: they are small and fast enough to be …

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer
operator) contain the essential information about the molecular thermodynamics and …

Markov state models (MSMs) have become the tool of choice to analyze large amounts of
molecular dynamics data by approximating them as a Markov jump process between …

The study of folding and conformational changes of macromolecules by molecular dynamics
simulations often requires the generation of large amounts of simulation data that are difficult …

Markov (state) models (MSMs) have attracted a lot of interest recently as they (1) can probe
long-term molecular kinetics based on short-time simulations,(2) offer a way to analyze great …

The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506
binding protein) is investigated by explicit water molecular dynamics simulations and …

Recent work has shown that the incorporation of an all-hydrocarbon “staple” into peptides
can greatly increase their α-helix propensity, leading to an improvement in pharmaceutical …