Markov state models (MSMs), which model conforma tional dynamics as a network of transitions between metastable states, have been increasingly used to model the thermodynamics and kinetics of biomolecules. In considering perturbations to molecular dynamics induced by sequence mutations, chemical modifications, or changes in external conditions, it is important to assess how transition rates change, independent of changes in metastable state definitions.
- Journal article: Surprisal Metrics for Quantifying Perturbed Conformational Dynamics in Markov State Models, Vincent A. Voelz, Brandon Elman, Asghar M. Razavi, and Guangfeng Zhou, Journal of Chemical Theory and Computation 10: 5716–5728, 2014
- Poster: Voelz, V., Elman, B., Razavi, A., & Zhou, G. Surprisal metrics for quantifying perturbed conformational dynamics in Markov state models. [PDF]