(Q33480934)

27 July 2017

title

Analysis of the free-energy surface of proteins from reversible folding simulations (English)

1 reference

27 July 2017

0 references

3

Emanuele Paci

1 reference

27 July 2017

Lucy R Allen

1

1 reference

27 July 2017

Sergei V Krivov

series ordinal

2

1 reference

27 July 2017

publication date

10 July 2009

1 reference

full work available at URL

27 July 2017

http://eprints.whiterose.ac.uk/10092/

content deliverer

White Rose Research Online

object has role

published version

copyright license

Creative Commons Attribution

0 references

https://doi.org/10.1371/journal.pcbi.1000428

copyright license

Creative Commons Attribution

object has role

published version

0 references

published in

PLOS Computational Biology

1 reference

27 July 2017

volume

5

1 reference

27 July 2017

issue

7

1 reference

27 July 2017

page(s)

e1000428

1 reference

Creative Commons Attribution 4.0 International

27 July 2017

copyright license

start time

10 July 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

CHARMM: the biomolecular simulation program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Identifying critical residues in protein folding: Insights from phi-value and P(fold) analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Diffusive reaction dynamics on invariant free energy profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Ab initio folding of proteins with all-atom discrete 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=2700257

One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: new insights into the folding process

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Origins of barriers and barrierless folding in BBL.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Parallel folding pathways in the SH3 domain 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=2700257

Secondary-structure analysis of denatured proteins by vacuum-ultraviolet circular dichroism 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=2700257

Backbone dynamics of the monomeric lambda repressor denatured state ensemble under nondenaturing conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Solvent-tuning the collapse and helix formation time scales of lambda(6-85)*.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Sequence of events in folding mechanism: beyond the Gō model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Atom-by-atom analysis of global downhill 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=2700257

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

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=2700257

Methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

The Yin and Yang of 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=2700257

A microscopic view of miniprotein folding: enhanced folding efficiency through formation of an intermediate

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

The experimental folding landscape of monomeric lactose repressor, a large two-domain protein, involves two kinetic intermediates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Characterization of the folding landscape of monomeric lactose repressor: quantitative comparison of theory and experiment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Nucleation and the transition state of the SH3 domain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Reaction coordinates and rates from transition paths

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Hidden complexity of free energy surfaces for peptide (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=2700257

Random-coil behavior and the dimensions of chemically unfolded proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Folding lambda-repressor at its speed limit

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

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=2700257

Direct molecular dynamics observation of protein folding transition state ensemble

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Validity of Gō models: comparison with a solvent-shielded empirical energy decomposition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Experimental identification of downhill 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=2700257

The origins of asymmetry in the folding transition states of protein L and protein G.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete 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=2700257

Intermediates can accelerate 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=2700257

Observation of strange kinetics in 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=2700257

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=2700257

Submillisecond folding of monomeric lambda repressor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

Specific intermediates in the folding reactions of small proteins and the mechanism of 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=2700257

Intermediates in the folding reactions of small proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

A model of myoglobin self-organization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2700257

One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Automatic method for identifying reaction coordinates in complex systems.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

One-dimensional free-energy profiles of complex systems: progress variables that preserve the barriers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Free-energy landscapes of proteins in the presence and absence of force

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Commitment and nucleation in the protein G transition state

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Stability and kinetic properties of C5-domain from myosin binding protein C and its mutants

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Tuning lambda6-85 towards downhill folding at its melting temperature

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Solvent viscosity dependence of the protein folding dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Persistence of native-like topology in a denatured protein in 8 M urea

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

On the transition coordinate for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

Folding at the speed limit

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000428

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

21 January 2018

1 reference

12 December 2020

The energy landscape of a fast-folding protein mapped by Ala-->Gly substitutions

1 reference

12 December 2020

Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions

1 reference

12 December 2020

Microsecond protein folding through a compact transition state

1 reference

12 December 2020

Native and non-native interactions along protein folding and unfolding pathways

1 reference

12 December 2020

Nanosecond folding dynamics of a three-stranded beta-sheet

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000428

Identifiers

DOI

1 reference

journals/ploscb/AllenKP09

27 July 2017

0 references

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

27 July 2017

1 reference