(Q35071957)

6 August 2017

title

The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel (English)

1 reference

6 August 2017

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Hongxing Lei

1

1 reference

6 August 2017

Changjun Chen

series ordinal

2

1 reference

6 August 2017

Yi Xiao

series ordinal

3

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6 August 2017

Yong Duan

series ordinal

4

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6 August 2017

language of work or name

English

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publication date

1 May 2011

1 reference

Journal of Chemical Physics

6 August 2017

published in

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6 August 2017

volume

134

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6 August 2017

issue

20

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6 August 2017

page(s)

205104

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describes a project that uses

6 August 2017

Cytoscape

1 reference

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

inferred from PubMed Central ID database lookup

cites work

Folding network of villin headpiece subdomain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Atomic-level characterization of the structural dynamics of proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Role of protein stabilizers on the conformation of the unfolded state of cytochrome c and its early folding kinetics: investigation at single molecular resolution.

8 July 2018

1 reference

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Protein folded states are kinetic hubs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Nanosecond time-resolved polarization spectroscopies: tools for probing protein reaction mechanisms

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Network models for molecular kinetics and their initial applications to human health

8 July 2018

1 reference

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Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Detection of a transient intermediate in a rapid protein folding process by solid-state nuclear magnetic resonance

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Common structural transitions in explicit-solvent simulations of villin headpiece folding

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Chemical, physical, and theoretical kinetics of an ultrafast folding protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Using an amino acid fluorescence resonance energy transfer pair to probe protein unfolding: application to the villin headpiece subdomain and the LysM domain

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Two-stage folding of HP-35 from ab initio simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Network and graph analyses of folding free energy surfaces

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

The Amber biomolecular simulation programs

8 July 2018

1 reference

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Finding pathways between distant local minima

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Exploring protein native states and large-scale conformational changes with a modified generalized born model

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Cytoscape: a software environment for integrated models of biomolecular interaction networks

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Native-like mean structure in the unfolded ensemble of small proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Toward an outline of the topography of a realistic protein-folding funnel

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Time-resolved small-angle X-ray scattering study of the folding dynamics of barnase

8 July 2018

1 reference

Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Improvements of network approach for analysis of the folding free-energy surface of peptides and proteins.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Folding of the villin headpiece subdomain from random structures. Analysis of the charge distribution as a function of pH.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3124538

Molecular dynamics with coupling to an external bath

27 September 2018

1 reference

Simple theory of protein folding kinetics

21 January 2018

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Ab initio folding of helix bundle proteins using molecular dynamics simulations

1 reference

12 December 2020

All-atom fast protein folding simulations: the villin headpiece

1 reference

12 December 2020

Free-Energy Landscape of the Villin Headpiece in an All-Atom Force Field

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.3596272

1 reference

6 August 2017

1 reference

6 August 2017

1 reference