(Q44539516)

4 December 2017

title

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics (English)

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4 December 2017

6

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4 December 2017

Yuan Yao

1

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4 December 2017

Raymond Z Cui

2

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4 December 2017

Gregory R Bowman

3

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4 December 2017

Daniel-Adriano Silva

4

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4 December 2017

Jian Sun

5

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4 December 2017

language of work or name

English

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publication date

1 May 2013

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Journal of Chemical Physics

4 December 2017

published in

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4 December 2017

volume

138

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4 December 2017

issue

17

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4 December 2017

page(s)

174106

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

4 December 2017

cites work

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MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

21 January 2018

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Coarse master equations for peptide folding dynamics.

21 January 2018

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

21 January 2018

1 reference

Transition networks for modeling the kinetics of conformational change in macromolecules

21 January 2018

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Simulating replica exchange simulations of protein folding with a kinetic network model

21 January 2018

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Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories

21 January 2018

1 reference

Rapid equilibrium sampling initiated from nonequilibrium data

21 January 2018

1 reference

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

21 January 2018

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Building Markov state models along pathways to determine free energies and rates of transitions

21 January 2018

1 reference

Markov state models based on milestoning.

21 January 2018

1 reference

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

21 January 2018

1 reference

Taming the complexity of protein folding

21 January 2018

1 reference

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

21 January 2018

1 reference

Simple few-state models reveal hidden complexity in protein folding

21 January 2018

1 reference

Modeling conformational ensembles of slow functional motions in Pin1-WW

21 January 2018

1 reference

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

21 January 2018

1 reference

A role for both conformational selection and induced fit in ligand binding by the LAO protein

21 January 2018

1 reference

Mechanisms of protein-ligand association and its modulation by protein mutations

21 January 2018

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Progress and challenges in the automated construction of Markov state models for full protein systems

21 January 2018

1 reference

Topological methods for exploring low-density states in biomolecular folding pathways

21 January 2018

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Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

21 January 2018

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Identifying Metastable States of Folding Proteins

21 January 2018

1 reference

A Bayesian method for construction of Markov models to describe dynamics on various time-scales

21 January 2018

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A fast parallel clustering algorithm for molecular simulation trajectories.

21 January 2018

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

21 January 2018

1 reference

Tryptophan zippers: Stable, monomeric -hairpins

21 January 2018

1 reference

Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations.

21 January 2018

1 reference

Detection-dependent kinetics as a probe of folding landscape microstructure

21 January 2018

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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

21 January 2018

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Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1063/1.4802007

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4 December 2017

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