Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

(2013) Benjamin Lindner et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9

(2013) Christian R. Schwantes et al.   Journal of Chemical Theory and Computation

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

(2013) Frank Noé et al.   MULTISCALE MODELING & SIMULATION

Limitations of Constant-Force-Feedback Experiments

(2012) Phillip J. Elms et al.   BIOPHYSICAL JOURNAL

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

(2012) Gregory R. Bowman   JOURNAL OF CHEMICAL PHYSICS

EMMA: A Software Package for Markov Model Building and Analysis

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

Estimating the Eigenvalue Error of Markov State Models

(2012) Natasa Djurdjevac et al.   MULTISCALE MODELING & SIMULATION

Simple few-state models reveal hidden complexity in protein folding

(2012) K. A. Beauchamp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

(2012) G. R. Bowman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

(2011) Bettina G. Keller et al.   CHEMICAL PHYSICS

Markov models of molecular kinetics: Generation and validation

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

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

(2011) F. Noe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

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

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

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On the Approximation Quality of Markov State Models

(2010) Marco Sarich et al.   MULTISCALE MODELING & SIMULATION

Experimental evidence for a frustrated energy landscape in a three-helix-bundle protein family

(2010) Beth G. Wensley et al.   NATURE

Full distance-resolved folding energy landscape of one single protein molecule

(2010) J. C. M. Gebhardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Nucleosome disassembly intermediates characterized by single-molecule FRET

(2009) A. Gansen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

(2009) Y. Santoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse Master Equations for Peptide Folding Dynamics†

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