(Q41585818)

4 October 2017

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. (English)

1 reference

4 October 2017

2

Vijay S Pande

1 reference

4 October 2017

Christian R Schwantes

series ordinal

1

1 reference

4 October 2017

1 April 2013

1 reference

4 October 2017

10

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Journal of Chemical Theory and Computation

inferred from page(s)

published in

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4 October 2017

9

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4 October 2017

4

1 reference

4 October 2017

2000-2009

1 reference

EMMA: A Software Package for Markov Model Building and Analysis.

4 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Evaluation and optimization of discrete state models of protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Simple few-state models reveal hidden complexity in protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

The role of atomic level steric effects and attractive forces in protein folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Equilibrium distribution from distributed computing (simulations of protein folding).

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Everything you wanted to know about Markov State Models but were afraid to ask

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Protein folded states are kinetic hubs

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Transition networks for modeling the kinetics of conformational change in macromolecules

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

COMPUTING: Screen Savers of the World Unite!

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Hidden complexity of free energy surfaces for peptide (protein) folding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

The effects of nonnative interactions on protein folding rates: theory and simulation

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Folding a protein in a computer: An atomic description of the folding/unfolding of protein A

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Prediction of folding mechanism for circular-permuted proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Helix nucleation kinetics from molecular simulations in explicit solvent

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Essential dynamics of proteins

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Navigating the folding routes

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Markov state models based on milestoning.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Markov models of molecular kinetics: generation and validation

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Subdomain competition, cooperativity, and topological frustration in the folding of CheY.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Dihedral angle principal component analysis of molecular dynamics simulations.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

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

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

What is the relation between slow feature analysis and independent component analysis?

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

A global geometric framework for nonlinear dimensionality reduction

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3673732

Energy landscape of a small peptide revealed by dihedral angle principal component analysis

19 August 2018

1 reference

12 December 2020

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein

1 reference

12 December 2020

Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

1 reference

12 December 2020

Separation of a mixture of independent signals using time delayed correlations

1 reference

12 December 2020

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis

1 reference

12 December 2020

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT300878A

1 reference

4 October 2017

1 reference

4 October 2017

1 reference

PMCID

3673732