Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information

A critical appraisal of Markov state models

(2015) Ch. Schütte et al.   European Physical Journal-Special Topics

Gaussian Markov transition models of molecular kinetics

(2015) Hao Wu et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic properties of force fields

(2015) F. Vitalini et al.   JOURNAL OF CHEMICAL PHYSICS

A Basis Set for Peptides for the Variational Approach to Conformational Kinetics

(2015) F. Vitalini et al.   Journal of Chemical Theory and Computation

Bottom-Up Coarse-Graining of Peptide Ensembles and Helix–Coil Transitions

(2015) Joseph F. Rudzinski et al.   Journal of Chemical Theory and Computation

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Microsecond protein dynamics observed at the single-molecule level

(2015) Takuhiro Otosu et al.   Nature Communications

Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

(2014) Kyle A. Beauchamp et al.   BIOPHYSICAL JOURNAL

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Variational Approach to Molecular Kinetics

(2014) Feliks Nüske et al.   Journal of Chemical Theory and Computation

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

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

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

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

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Microsecond dynamics of an unfolded protein by a line confocal tracking of single molecule fluorescence

(2013) Hiroyuki Oikawa et al.   Scientific Reports

EMMA: A Software Package for Markov Model Building and Analysis

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

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

(2012) Elio A. Cino et al.   Journal of Chemical Theory and Computation

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development

(2012) Fan Jiang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

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

Single-Molecule Fluorescence Experiments Determine Protein Folding Transition Path Times

(2012) H. S. Chung et al.   SCIENCE

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

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

Studying functional dynamics in bio-molecules using accelerated molecular dynamics

(2011) Phineus R. L. Markwick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions

(2011) Bartosz Różycki et al.   STRUCTURE

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

(2010) Oliver F. Lange et al.   BIOPHYSICAL JOURNAL

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

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

Observation uncertainty in reversible Markov chains

(2010) Philipp Metzner et al.   PHYSICAL REVIEW E

Improved side-chain torsion potentials for the Amber ff99SB protein force field

(2010) Kresten Lindorff-Larsen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Generic coarse-grained model for protein folding and aggregation

(2009) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Probability distributions of molecular observables computed from Markov models

(2008) Frank Noé   JOURNAL OF CHEMICAL PHYSICS