(Q44385234)

2 December 2017

title

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

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2 December 2017

John D Chodera

1

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2 December 2017

Frank Noé

series ordinal

2

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2 December 2017

language of work or name

English

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publication date

1 September 2010

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Journal of Chemical Physics

2 December 2017

published in

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2 December 2017

volume

133

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2 December 2017

issue

10

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2 December 2017

page(s)

105102

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Transition networks for modeling the kinetics of conformational change in macromolecules

2 December 2017

cites work

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Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

21 January 2018

1 reference

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

21 January 2018

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Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states.

21 January 2018

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Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data

21 January 2018

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Validation of Markov state models using Shannon's entropy.

21 January 2018

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Coarse master equations for peptide folding dynamics.

21 January 2018

1 reference

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

21 January 2018

1 reference

Probability distributions of molecular observables computed from Markov models.

21 January 2018

1 reference

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

21 January 2018

1 reference

Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics

21 January 2018

1 reference

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

21 January 2018

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Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

21 January 2018

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Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

21 January 2018

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Inference from Iterative Simulation Using Multiple Sequences

21 January 2018

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An invariant form for the prior probability in estimation problems

21 January 2018

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Single-molecule fluorescence studies of protein folding and conformational dynamics

21 January 2018

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Single-molecule fluorescence spectroscopy of protein folding.

21 January 2018

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Branching out of single-molecule fluorescence spectroscopy: challenges for chemistry and influence on biology

21 January 2018

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Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent

21 January 2018

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Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding.

21 January 2018

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Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy.

21 January 2018

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Fluorescence quenching of dyes by tryptophan: interactions at atomic detail from combination of experiment and computer simulation

21 January 2018

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GROMACS: A message-passing parallel molecular dynamics implementation

21 January 2018

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GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

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The missing term in effective pair potentials

21 January 2018

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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

A solution for the best rotation to relate two sets of vectors

21 January 2018

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A discussion of the solution for the best rotation to relate two sets of vectors

21 January 2018

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Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

21 January 2018

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The GROMOS Biomolecular Simulation Program Package

21 January 2018

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Fluctuation formulas in molecular-dynamics simulations with the weak coupling heat bath

21 January 2018

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Molecular dynamics with coupling to an external bath

21 January 2018

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Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.3463406

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2 December 2017

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