(Q37330270)

19 August 2017

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

1 reference

19 August 2017

4

Martin Karplus

1 reference

19 August 2017

Stefanie Muff

2

0 references

Amedeo Caflisch

series ordinal

3

object named as

Amedeo Caflisch

1 reference

19 August 2017

Sergei V Krivov

1

1 reference

PMC publication ID

2736680

19 August 2017

language of work or name

English

0 references

publication date

1 July 2008

1 reference

19 August 2017

14

1 reference

Journal of Physical Chemistry B

inferred from page(s)

published in

1 reference

19 August 2017

112

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19 August 2017

29

1 reference

19 August 2017

8701-8714

1 reference

A stable alpha-helix-rich intermediate is formed by a single mutation of the beta-sheet protein, src SH3, at pH 3.

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

An alpha-helical burst in the src SH3 folding pathway

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Understanding ensemble protein folding at atomic detail

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Kinetic definition of protein folding transition state ensembles and reaction coordinates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Network and graph analyses of folding free energy surfaces

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Progress in modeling of protein structures and interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Ensemble versus single-molecule protein unfolding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Reaction coordinates and rates from transition paths

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Energy landscapes and solved protein-folding problems.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Phi-value analysis by molecular dynamics simulations of reversible folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Hidden complexity of free energy surfaces for peptide (protein) folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Rationalization of the effects of mutations on peptide and protein aggregation rates.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The present view of the mechanism of protein folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Experimental identification of downhill protein folding.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

A structure-based method for derivation of all-atom potentials for protein folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Protein folding and unfolding at atomic resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Evaluation of a fast implicit solvent model for molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Protein folding theory: from lattice to all-atom models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Three key residues form a critical contact network in a protein folding transition state

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Folding simulations of a three-stranded antiparallel beta -sheet peptide

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Fast kinetics and mechanisms in protein folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Understanding protein folding via free-energy surfaces from theory and experiment

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

De novo design of a monomeric three-stranded antiparallel beta-sheet

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Folding dynamics and mechanism of beta-hairpin formation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Funnels, pathways, and the energy landscape of protein folding: a synthesis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The Energy Landscapes and Motions of Proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The folding of hen lysozyme involves partially structured intermediates and multiple pathways

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

The early folding kinetics of apomyoglobin

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

1 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Wordom: a program for efficient analysis of molecular dynamics simulations.

1 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Commitment and nucleation in the protein G transition state

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

How do small single-domain proteins fold?

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Noninteracting local‐structure model of folding and unfolding transition in globular proteins. I. Formulation

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2736680

Weak temperature dependence of the free energy surface and folding pathways of structured peptides

2 September 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

The protein folding network

1 reference

12 December 2020

Estimation of protein folding probability from equilibrium simulations

1 reference

12 December 2020

A lattice protein with an amyloidogenic latent state: stability and folding kinetics

1 reference

12 December 2020

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single-point mutation of a beta-sheet miniprotein

1 reference

12 December 2020

Protein Folding: A Perspective from Theory and Experiment.

1 reference

12 December 2020

Submillisecond kinetics of protein folding

1 reference

12 December 2020

Simulation of activation free energies in molecular systems

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP711864R

Maximal flow through a network

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP711864R

On the transition coordinate for protein folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP711864R

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JP711864R

Identifiers

DOI

10.1021/JP711864R

1 reference

19 August 2017

1 reference

PMC publication ID

2736680

19 August 2017

PubMed publication ID

18590307

1 reference

PMC publication ID

2736680