Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments (Q34201529)

31 July 2017

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

1 reference

31 July 2017

Rhiju Das

3

0 references

Vijay Pande

series ordinal

4

object named as

Vijay S Pande

1 reference

31 July 2017

1

Kyle A Beauchamp

1 reference

31 July 2017

Daniel L Ensign

2

1 reference

PubMed ID

21768345

31 July 2017

language of work or name

English

0 references

publication date

18 July 2011

1 reference

Proceedings of the National Academy of Sciences of the United States of America

31 July 2017

1 reference

31 July 2017

108

1 reference

31 July 2017

31

1 reference

31 July 2017

12734-12739

1 reference

How robust are protein folding simulations with respect to force field parameterization?

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Making connections between ultrafast protein folding kinetics and 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=3150881

Protein folded states are kinetic hubs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

An unlocking/relocking barrier in conformational fluctuations of 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=3150881

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium 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=3150881

Common structural transitions in explicit-solvent simulations of villin headpiece 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=3150881

Progress and challenges in the automated construction of Markov state models for full protein systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Native like structure in the unfolded state of the villin headpiece helical subdomain, 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=3150881

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=3150881

Using generalized ensemble simulations and Markov state models to identify conformational states

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Accelerating molecular dynamic simulation on graphics processing units

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Transition networks for modeling the kinetics of conformational change in macromolecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Urea and guanidinium chloride denature protein L in different ways 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=3150881

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=3150881

Anatomy of energetic changes accompanying urea-induced protein denaturation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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=3150881

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=3150881

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=3150881

Determination of ultrafast protein folding rates from loop formation dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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=3150881

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=3150881

Absolute comparison of simulated and experimental protein-folding dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

Measuring the rate of intramolecular contact formation in 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=3150881

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

NMR structure of the 35-residue 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=3150881

Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3150881

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

5 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1010880108

First-principles calculations of protein circular dichroism in the near ultraviolet.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1010880108

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1010880108

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1010880108

A thermostable 35-residue subdomain within villin headpiece

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21768345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1010880108

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference

PubMed ID

21768345