(Q37087946)

English

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow

scientific article published on 15 May 2013

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: application to a hydrodynamic analysis of the folding flow (English)

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

4

object named as

Martin Karplus

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Amedeo Caflisch

2

object named as

Amedeo Caflisch

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

author name string

Igor V Kalgin

1

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Sergei F Chekmarev

3

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

language of work or name

0 references

publication date

15 May 2013

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

Journal of Physical Chemistry B

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

117

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

20

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

6092-6105

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

How fast-folding proteins fold

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740565

29 September 2017

Turbulent phenomena in protein folding

1 reference

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29 September 2017

Kinetic network study of the diversity and temperature dependence of Trp-Cage folding pathways: combining transition path theory with stochastic simulations

1 reference

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29 September 2017

Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study

1 reference

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29 September 2017

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

1 reference

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29 September 2017

Folding of a SH3 domain: standard and "hydrodynamic" analyses

1 reference

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29 September 2017

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

1 reference

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29 September 2017

Folding energy landscape and network dynamics of small globular proteins

1 reference

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29 September 2017

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

1 reference

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29 September 2017

Kinetic definition of protein folding transition state ensembles and reaction coordinates

1 reference

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Hessian eigenmaps: locally linear embedding techniques for high-dimensional data

1 reference

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29 September 2017

Phi-value analysis by molecular dynamics simulations of reversible folding

1 reference

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29 September 2017

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

1 reference

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29 September 2017

Continuum secondary structure captures protein flexibility

1 reference

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29 September 2017

Evaluation of a fast implicit solvent model for molecular dynamics simulations

1 reference

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29 September 2017

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

1 reference

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29 September 2017

Nonlinear dimensionality reduction by locally linear embedding

1 reference

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29 September 2017

Folding simulations of a three-stranded antiparallel beta -sheet peptide

1 reference

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29 September 2017

Fast kinetics and mechanisms in protein folding

1 reference

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29 September 2017

Understanding protein folding via free-energy surfaces from theory and experiment

1 reference

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29 September 2017

De novo design of a monomeric three-stranded antiparallel beta-sheet

1 reference

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29 September 2017

Theory of protein folding: the energy landscape perspective

1 reference

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29 September 2017

Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural networks

1 reference

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29 September 2017

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

1 reference

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27 June 2018

Determination of reaction coordinates via locally scaled diffusion map.

1 reference

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3 September 2018

Identification of the protein folding transition state from molecular dynamics trajectories.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740565

3 September 2018

ETNA: equilibrium transitions network and Arrhenius equation for extracting folding kinetics from REMD simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740565

3 September 2018

Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3740565

3 September 2018

Wordom: a program for efficient analysis of molecular dynamics simulations.

1 reference

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3 September 2018

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

1 reference

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3 September 2018

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

1 reference

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3 September 2018

A global geometric framework for nonlinear dimensionality reduction

1 reference

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3 September 2018

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

1 reference

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12 December 2020

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The protein folding network

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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Estimation of protein folding probability from equilibrium simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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A lattice protein with an amyloidogenic latent state: stability and folding kinetics

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https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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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

https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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Full correlation analysis of conformational protein dynamics

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

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Hydrodynamic description of protein folding

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

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Extracting physically intuitive reaction coordinates from transition networks of a beta-sheet miniprotein

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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Delineation of folding pathways of a β-sheet miniprotein

1 reference

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Distribution of Reciprocal of Interatomic Distances: A Fast Structural Metric

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

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Protein Folding: A Perspective from Theory and Experiment.

1 reference

https://pubmed.ncbi.nlm.nih.gov/23621790

12 December 2020

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Free Energy Guided Sampling

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11 October 2022

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

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CHARMM: the biomolecular simulation program

1 reference

11 October 2022

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On the transition coordinate for protein folding

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11 October 2022

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Identifiers

10.1021/JP401742Y

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

18 August 2017

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