Markov state model reveals folding and functional dynamics in ultra-long MD trajectories (Q24633443)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21988563%20AND%20SRC:MED&resulttype=core&format=json

14 February 2020

title

Markov state model reveals folding and functional dynamics in ultra-long MD trajectories (English)

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14 February 2020

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4

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14 February 2020

5

Vijay S Pande

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14 February 2020

3

Kyle Beauchamp

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14 February 2020

author name string

Thomas J Lane

series ordinal

1

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14 February 2020

Gregory R Bowman

series ordinal

2

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14 February 2020

language of work or name

English

0 references

publication date

26 October 2011

1 reference

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Journal of the American Chemical Society

14 February 2020

number of pages

7

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based on heuristic

inferred from page(s)

published in

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14 February 2020

volume

133

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14 February 2020

issue

45

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14 February 2020

page(s)

18413-18419

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

14 February 2020

cites work

1 reference

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

7 April 2017

1 reference

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Structure-function-folding relationship in a WW domain

7 April 2017

1 reference

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Modeling conformational ensembles of slow functional motions in Pin1-WW

7 April 2017

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1H NMR study on the binding of Pin1 Trp-Trp domain with phosphothreonine peptides

7 April 2017

1 reference

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

7 April 2017

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The protein folding problem

7 April 2017

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Atomic-Level Characterization of the Structural Dynamics of Proteins

7 April 2017

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The role of dynamic conformational ensembles in biomolecular recognition

7 April 2017

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Enhanced modeling via network theory: Adaptive sampling of Markov state models

7 April 2017

1 reference

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MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

27 September 2017

1 reference

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Protein folded states are kinetic hubs

27 September 2017

1 reference

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

27 September 2017

1 reference

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

27 September 2017

1 reference

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Reactive flux and folding pathways in network models of coarse-grained protein dynamics

27 September 2017

1 reference

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

27 September 2017

1 reference

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Transition networks for modeling the kinetics of conformational change in macromolecules

27 September 2017

1 reference

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An experimental survey of the transition between two-state and downhill protein folding scenarios

27 September 2017

1 reference

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Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece

27 September 2017

1 reference

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Theory of protein folding

27 September 2017

1 reference

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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

27 September 2017

1 reference

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The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential

27 September 2017

1 reference

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Atomistic folding simulations of the five-helix bundle protein λ(6−85).

30 May 2018

1 reference

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The Fip35 WW domain folds with structural and mechanistic heterogeneity in molecular dynamics simulations

30 May 2018

1 reference

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

30 May 2018

1 reference

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The transition state transit time of WW domain folding is controlled by energy landscape roughness

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21988563

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Sequence-specific dynamics modulate recognition specificity in WW domains

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21988563

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12 December 2020

based on heuristic

Identifiers

DOI

10.1021/JA207470H

2 references

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14 February 2020

1 reference

2 references

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14 February 2020

PubMed publication ID

21988563

2 references