Markov models of molecular kinetics: Generation and validation

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

(2010) John D. Chodera 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

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

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

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

Multidimensional Langevin modeling of biomolecular dynamics

(2009) Rainer Hegger et al.   JOURNAL OF CHEMICAL PHYSICS

Progress and challenges in the automated construction of Markov state models for full protein systems

(2009) Gregory R. Bowman et al.   JOURNAL OF CHEMICAL PHYSICS

Topological methods for exploring low-density states in biomolecular folding pathways

(2009) Yuan Yao et al.   JOURNAL OF CHEMICAL PHYSICS

Data-Based Inference of Generators for Markov Jump Processes Using Convex Optimization

(2009) Daan Crommelin et al.   MULTISCALE MODELING & SIMULATION

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Estimating the sampling error: Distribution of transition matrices and functions of transition matrices for given trajectory data

(2009) Philipp Metzner et al.   PHYSICAL REVIEW E

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

Molecular simulation as an aid to experimentalists

(2008) Wilfred F van Gunsteren et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Transition networks for modeling the kinetics of conformational change in macromolecules

(2008) Frank Noé et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Combining experiment and simulation in protein folding: closing the gap for small model systems

(2008) R Dustin Schaeffer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ruggedness in the folding landscape of protein L

(2008) Steven A. Waldauer et al.   HFSP Journal

Building Markov state models along pathways to determine free energies and rates of transitions

(2008) Albert C. Pan et al.   JOURNAL OF CHEMICAL PHYSICS

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics

(2008) Ben Cooke et al.   JOURNAL OF CHEMICAL PHYSICS

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations

(2008) Cristian Micheletti et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

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