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

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

(2013) Zheng Yi et al.   JOURNAL OF CHEMICAL PHYSICS

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

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

Sassena — X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers

(2012) Benjamin Lindner et al.   COMPUTER PHYSICS COMMUNICATIONS

EMMA: A Software Package for Markov Model Building and Analysis

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

nMoldyn 3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations

(2012) Konrad Hinsen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent

(2012) Xiang-qiang Chu et al.   Journal of Physical Chemistry Letters

Estimating the Eigenvalue Error of Markov State Models

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

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

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 State Models of Millisecond Folder ACBP Reveals New Views of the Folding Reaction

(2011) Vincent A. Voelz et al.   BIOPHYSICAL JOURNAL

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 state models based on milestoning

(2011) Christof Schütte et al.   JOURNAL OF CHEMICAL PHYSICS

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

Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables

(2011) Jan-Hendrik Prinz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The amino acid dipeptide: Small but still influential after 50 years

(2011) J. Hermans   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

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

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

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

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

On the Approximation Quality of Markov State Models

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

Dynamics of a protein and its surrounding environment: A quasielastic neutron scattering study of myoglobin in water and glycerol mixtures

(2009) H. Jansson et al.   JOURNAL OF CHEMICAL PHYSICS

Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics

(2009) M.-P. Gaigeot   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

In Vivo Measurement of Internal and Global Macromolecular Motions in Escherichia coli

(2008) M. Jasnin et al.   BIOPHYSICAL JOURNAL

Transition networks for modeling the kinetics of conformational change in macromolecules

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

Down to atomic-scale intracellular water dynamics

(2008) Marion Jasnin et al.   EMBO JOURNAL

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS

Coarse Master Equations for Peptide Folding Dynamics†

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