Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution

EMMA: A Software Package for Markov Model Building and Analysis

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

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

(2012) P. Soderhjelm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Kinetic characterization of the critical step in HIV-1 protease maturation

(2012) S. K. Sadiq 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

Mechanisms of Protein-Ligand Association and Its Modulation by Protein Mutations

(2011) Martin Held et al.   BIOPHYSICAL JOURNAL

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

Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach

(2011) Wei Zhuang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories

(2011) Thomas J. Lane et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes

(2011) Jan-Hendrik Prinz et al.   MULTISCALE MODELING & SIMULATION

The social network (of protein conformations)

(2011) John D. Chodera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations

(2011) I. Buch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

(2011) K. A. Beauchamp 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

The Free Energy Landscape of Small Molecule Unbinding

(2011) Danzhi Huang et al.   PLoS Computational Biology

Taming the complexity of protein folding

(2010) Gregory R Bowman et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Enhanced sampling and applications in protein folding in explicit solvent

(2010) Cheng Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

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

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

Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6−85

(2010) Gregory R. Bowman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On the Approximation Quality of Markov State Models

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

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

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

(2009) Sergio Bacallado 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

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

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

Using Markov Models to Simulate Electron Spin Resonance Spectra from Molecular Dynamics Trajectories

(2008) Deniz Sezer et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin

(2007) Angel E. Garcia et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY