(Q34704233)

4 August 2017

title

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

1 reference

4 August 2017

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3

Vijay S Pande

1 reference

4 August 2017

Daniel L Ensign

1

1 reference

4 August 2017

Peter M Kasson

series ordinal

2

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4 August 2017

language of work or name

English

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publication date

29 September 2007

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4 August 2017

number of pages

11

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Journal of Molecular Biology

inferred from page(s)

published in

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4 August 2017

volume

374

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4 August 2017

issue

3

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4 August 2017

page(s)

806-816

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COMPUTING: Screen Savers of the World Unite!

4 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Sub-microsecond protein folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

How well can simulation predict protein folding kinetics and thermodynamics?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Folding lambda-repressor at its speed limit

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Simulations of the role of water in the protein-folding mechanism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Fast and faster: a designed variant of the B-domain of protein A folds in 3 microsec

7 July 2018

1 reference

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Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Experimental tests of villin subdomain folding simulations

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Experimental identification of downhill protein folding.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Absolute comparison of simulated and experimental protein-folding dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

The role of aromatic residues in the hydrophobic core of the villin headpiece subdomain

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Searching for "downhill scenarios" in protein folding

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Canonical dynamics: Equilibrium phase-space distributions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

VMD: visual molecular dynamics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Dominant pathways in protein folding.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Engineering a beta-sheet protein toward the folding speed limit.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Validation of Markov state models using Shannon's entropy.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Error analysis and efficient sampling in Markovian state models for molecular dynamics.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Solution structure of a protein denatured state and folding intermediate.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Rate-temperature relationships in lambda-repressor fragment lambda 6-85 folding

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

Peptide models provide evidence for significant structure in the denatured state of a rapidly folding protein: the villin headpiece subdomain

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

The denatured state of Engrailed Homeodomain under denaturing and native conditions.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3689540

All-atom fast protein folding simulations: the villin headpiece

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17950314

12 December 2020

inferred from PubMed ID database lookup

Folding at the speed limit

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17950314

12 December 2020

inferred from PubMed ID database lookup

Nanosecond folding dynamics of a three-stranded beta-sheet

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17950314

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1016/J.JMB.2007.09.069

1 reference

4 August 2017

1 reference

4 August 2017

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