Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data (Q31028368)

14 September 2017

Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data (English)

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molecular dynamics simulation

14 September 2017

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609791%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609791%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Athanasios S Baltzis

1 reference

14 September 2017

Nicholas M Glykos

series ordinal

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14 September 2017

26 November 2015

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14 September 2017

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8 June 2020

volume

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8 June 2020

issue

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8 June 2020

page(s)

587-596

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Balanced Protein-Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

8 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

On the application of Good-Turing statistics to quantify convergence of biomolecular simulations.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Three force fields' views of the 3(10) helix.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Folding Network of Villin Headpiece Subdomain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Enhanced sampling and applications in protein folding in explicit solvent

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Improved side-chain torsion potentials for the Amber ff99SB protein force field

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Native like structure in the unfolded state of the villin headpiece helical subdomain, an ultrafast folding protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Slow motions in chicken villin headpiece subdomain probed by cross-correlated NMR relaxation of amide NH bonds in successive residues

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Raster3D: photorealistic molecular graphics

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

21 June 2018

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

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Sub-microsecond protein folding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Electrostatics calculations: latest methodological advances

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Scalable molecular dynamics with NAMD

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

The Amber biomolecular simulation programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

WebLogo: A Sequence Logo Generator

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Experimental tests of villin subdomain folding simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

NMR structure of the 35-residue villin headpiece subdomain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Knowledge-based protein secondary structure assignment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4815414

Comparison of simple potential functions for simulating liquid water

21 June 2018

1 reference

Using J-coupling constants for force field validation: application to hepta-alanine.

21 January 2018

1 reference

On the foldability of tryptophan-containing tetra- and pentapeptides: an exhaustive molecular dynamics study.

21 January 2018

1 reference

Kinetic network models of tryptophan mutations in β-hairpins reveal the importance of non-native interactions.

21 January 2018

1 reference

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

21 January 2018

1 reference

Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

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

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories.

21 January 2018

1 reference

Dihedral angle principal component analysis of molecular dynamics simulations.

21 January 2018

1 reference

Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis

21 January 2018

1 reference

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

21 January 2018

1 reference

12 December 2020

NMR Characterization of a Peptide Model Provides Evidence for Significant Structure in the Unfolded State of the Villin Headpiece Helical Subdomain†

1 reference

12 December 2020

Dynamic NMR Line-Shape Analysis Demonstrates that the Villin Headpiece Subdomain Folds on the Microsecond Time Scale

1 reference

12 December 2020

A thermostable 35-residue subdomain within villin headpiece

1 reference

12 December 2020

Software news and updates. Carma: a molecular dynamics analysis program

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

Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1002/PRO.2850

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609791%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609791%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

PubMed publication ID

26609791

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609791%20AND%20SRC:MED&resulttype=core&format=json