In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …

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 …

Proteins fold into unique native structures stabilized by thousands of weak interactions that
collectively overcome the entropic cost of folding. Although these forces are “encoded” in the …

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 …

Molecular dynamics (MD) simulations are widely used to study protein motions at an atomic
level of detail, but they have been limited to time scales shorter than those of many …

Characterizing the equilibrium ensemble of folding pathways, including their relative
probability, is one of the major challenges in protein folding theory today. Although this …

Markov state models provide a framework for understanding the fundamental states and
rates in the conformational dynamics of biomolecules. We describe an improved protocol for …

The millisecond time scale needed for molecular dynamics simulations to approach the
quantitative study of protein folding is not yet routine. One approach to extend the simulation …

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 …