Residue-specific α-helix propensities from molecular simulation (Q35843475)

10 August 2017

Residue-specific α-helix propensities from molecular simulation (English)

1 reference

10 August 2017

David de Sancho

2

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Robert B. Best

object named as

Robert B Best

series ordinal

1

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author name string

Jeetain Mittal

series ordinal

3

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PMCID

3309278

10 August 2017

language of work or name

English

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publication date

20 March 2012

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10 August 2017

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10 August 2017

102

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10 August 2017

1462-1467

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10 August 2017

6

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

How fast-folding proteins fold

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Speed limit of protein folding evidenced in secondary structure dynamics

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Direct assessment of the α-helix nucleation time

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Evaluating molecular mechanical potentials for helical peptides and proteins

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Context-independent, temperature-dependent helical propensities for amino acid residues

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Primary peptide folding dynamics observed with ultrafast temperature jump

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Local conformational dynamics in alpha-helices measured by fast triplet transfer

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Are current molecular dynamics force fields too helical?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

The alpha-helix folds on the millisecond time scale

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Unusually stable helix formation in short alanine-based peptides

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Coarse-graining errors and numerical optimization using a relative entropy framework

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

A general purpose model for the condensed phases of water: TIP4P/2005

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Helix-coil transitions re-visited

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

A refined solution structure of hen lysozyme determined using residual dipolar coupling data

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

The penultimate rotamer library

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3309278

Conformational Analysis of Macromolecules. IV. Helical Structures of Poly-L-Alanine, Poly-L-Valine, Poly-β-Methyl-L-Aspartate, Poly-γ-Methyl-L-Glutamate, and Poly-L-Tyrosine

24 September 2018

1 reference

12 December 2020

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

1 reference

12 December 2020

What Is the Time Scale for α-Helix Nucleation?

1 reference

12 December 2020

Balance between α and β Structures in Ab Initio Protein Folding

1 reference

12 December 2020

10.1016/J.BPJ.2012.02.024

Identifiers

DOI

1 reference

10 August 2017

1 reference

10 August 2017

1 reference

PMCID

3309278