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

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

(2013) Benjamin Lindner 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

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

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

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

(2011) Vincent A. Voelz 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

An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles

(2011) Bettina Keller et al.   Journal of Chemical Theory and Computation

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

Three Classes of Motion in the Dynamic Neutron-Scattering Susceptibility of a Globular Protein

(2011) Liang Hong et al.   PHYSICAL REVIEW LETTERS

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

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

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

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

(2009) Gregory R. Bowman et al.   METHODS

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

Transition networks for modeling the kinetics of conformational change in macromolecules

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

Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin

(2008) M. Krishnan et al.   JOURNAL OF PHYSICAL CHEMISTRY B