Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water (Q34032669)

30 July 2017

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water (English)

1 reference

30 July 2017

0 references

1 reference

Robert B Best

2

0 references

author name string

Jeetain Mittal

series ordinal

1

1 reference

PubMed ID

20682244

30 July 2017

language of work or name

English

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publication date

1 August 2010

1 reference

30 July 2017

1 reference

30 July 2017

99

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30 July 2017

3

1 reference

30 July 2017

L26-8

1 reference

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

30 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Force field bias in protein folding simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Blind test of physics-based prediction of protein structures.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Are current molecular dynamics force fields too helical?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Comparison of multiple Amber force fields and development of improved protein backbone parameters

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Recent successes of the energy landscape theory of protein folding and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Structure-function-folding relationship in a WW domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Sub-microsecond protein folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Effect of modulating unfolded state structure on the folding kinetics of the villin headpiece subdomain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

The protein folding 'speed limit'.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Unifying features in protein-folding mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Experimental tests of villin subdomain folding simulations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Smaller and faster: the 20-residue Trp-cage protein folds in 4 micros

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Mapping the transition state of the WW domain beta-sheet.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Mapping the transition state and pathway of protein folding by protein engineering

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Improved treatment of the protein backbone in empirical force fields.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2913180

Temperature-dependent Dynamics of the Villin Headpiece Helical Subdomain, An Unusually Small Thermostable Protein

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20682244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A thermostable 35-residue subdomain within villin headpiece

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20682244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The folding mechanism of a beta-sheet: the WW domain

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20682244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2010.05.005

1 reference

30 July 2017

1 reference

30 July 2017

1 reference

PubMed ID

20682244