Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

EMMA: A Software Package for Markov Model Building and Analysis

(2012) Martin Senne et al.   Journal of Chemical Theory and Computation

Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

(2012) Andreas Vitalis et al.   Journal of Chemical Theory and Computation

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

(2011) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Mapping the dynamics of multi-dimensional systems onto a nearest-neighbor coupled discrete set of states conserving the mean first-passage times: a projective dynamics approach

(2011) Katja Biswas et al.   Journal of Physics A-Mathematical and Theoretical

Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics

(2011) Gavin E Crooks et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Network models for molecular kinetics and their initial applications to human health

(2010) Gregory R Bowman et al.   CELL RESEARCH

Functional versus folding landscapes: the same yet different

(2010) Pavel I Zhuravlev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A Bayesian method for construction of Markov models to describe dynamics on various time-scales

(2010) Emily K. Rains et al.   JOURNAL OF CHEMICAL PHYSICS

Comparing geometric and kinetic cluster algorithms for molecular simulation data

(2010) Bettina Keller et al.   JOURNAL OF CHEMICAL PHYSICS

Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models

(2010) Gregory R. Bowman et al.   Journal of Chemical Theory and Computation

Protein folded states are kinetic hubs

(2010) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

(2009) Sergio Bacallado et al.   JOURNAL OF CHEMICAL PHYSICS

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Coarse Master Equations for Peptide Folding Dynamics†

(2008) Nicolae-Viorel Buchete et al.   JOURNAL OF PHYSICAL CHEMISTRY B