A directed essential dynamics simulation of peptide folding (Q34190165)

31 July 2017

title

A directed essential dynamics simulation of peptide folding (English)

1 reference

31 July 2017

Changjun Chen

1

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31 July 2017

Yi Xiao

series ordinal

2

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31 July 2017

Linsen Zhang

series ordinal

3

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31 July 2017

language of work or name

English

0 references

publication date

24 February 2005

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31 July 2017

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31 July 2017

volume

88

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31 July 2017

issue

5

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31 July 2017

page(s)

3276-3285

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Molecular dynamics simulations of peptides and proteins with amplified collective motions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Molecular dynamics simulations of protein folding from the transition state

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Enzyme specificity under dynamic control II: Principal component analysis of alpha-lytic protease using global and local solvent boundary conditions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Protein folding theory: from lattice to all-atom models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Anisotropy of fluctuation dynamics of proteins with an elastic network model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Efficient electrostatic solvation model for protein-fragment docking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Three-helix-bundle protein in a Ramachandran model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Stability and stabilization of globular proteins in 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=1305476

A sensitive assay of translational fidelity (readthrough and termination) in eukaryotic cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Investigating protein dynamics in collective coordinate space

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

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=1305476

An efficient method for sampling the essential subspace of proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Empirical scale of side-chain conformational entropy in 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=1305476

Engineering of stable and fast-folding sequences of model proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Essential dynamics of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Evolution-like selection of fast-folding model proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Dynamics of a small globular protein in terms of low-frequency vibrational modes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Molecular dynamics simulations of the unfolding of an alpha-helical analogue of ribonuclease A S-peptide in water

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Protein folding funnels: a kinetic approach to the sequence-structure relationship

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Increasing temperature accelerates protein unfolding without changing the pathway of 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=1305476

Essential dynamics of reversible peptide folding: memory-free conformational dynamics governed by internal hydrogen bonds.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305476

Essential Dynamics from NMR Clusters: Dynamic Properties of the Myb DNA-Binding Domain and a Hinge-Bending Enhancing Variant

28 October 2018

1 reference

12 December 2020

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis

1 reference

12 December 2020

Structure-based thermodynamic scale of alpha-helix propensities in amino acids

1 reference

12 December 2020

Solvent isotope effect and protein stability

1 reference

12 December 2020

First-principles calculation of the folding free energy of a three-helix bundle protein

1 reference

12 December 2020

Beta-hairpin folding simulations in atomistic detail using an implicit solvent model

1 reference

12 December 2020

The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water

1 reference

12 December 2020

Polymer principles of protein calorimetric two-state cooperativity

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

Hinge-bending motions in annexins: molecular dynamics and essential dynamics of apo-annexin V and of calcium bound annexin V and I

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.046904

Identifiers

DOI

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31 July 2017

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31 July 2017

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