Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides (Q33465189)

27 July 2017

title

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

1 reference

27 July 2017

Robert B Best

1

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Gerhard Hummer

object named as

Gerhard Hummer

series ordinal

2

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language of work or name

English

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publication date

1 July 2009

1 reference

Journal of Physical Chemistry B

27 July 2017

published in

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27 July 2017

volume

113

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27 July 2017

issue

26

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27 July 2017

page(s)

9004-9015

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Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

27 July 2017

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21 June 2018

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21 June 2018

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Are current molecular dynamics force fields too helical?

21 June 2018

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Ten-microsecond molecular dynamics simulation of a fast-folding WW domain

21 June 2018

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Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

21 June 2018

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Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations

21 June 2018

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The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations

21 June 2018

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

21 June 2018

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Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides

21 June 2018

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Energetic characterization of short helical polyalanine peptides in water: analysis of 13C=O chemical shift data

21 June 2018

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Simulations of the pressure and temperature unfolding of an alpha-helical peptide.

21 June 2018

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Exploring the helix-coil transition via all-atom equilibrium ensemble simulations

21 June 2018

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Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

21 June 2018

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21 June 2018

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An empirical backbone-backbone hydrogen-bonding potential in proteins and its applications to NMR structure refinement and validation.

21 June 2018

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Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations

21 June 2018

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The protein folding 'speed limit'.

21 June 2018

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Force fields for protein simulations

21 June 2018

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

21 June 2018

1 reference

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Structure validation by Calpha geometry: phi,psi and Cbeta deviation

21 June 2018

1 reference

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Intrinsically unstructured proteins

21 June 2018

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Polyproline II structure in a sequence of seven alanine residues.

21 June 2018

1 reference

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Helix formation via conformation diffusion search

21 June 2018

1 reference

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

21 June 2018

1 reference

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Dipolar couplings in macromolecular structure determination

21 June 2018

1 reference

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Order matrix analysis of residual dipolar couplings using singular value decomposition.

21 June 2018

1 reference

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Laser Temperature Jump Study of the Helix⇌Coil Kinetics of an Alanine Peptide Interpreted with a ‘Kinetic Zipper' Model

21 June 2018

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Comparison of NH Exchange and Circular Dichroism as Techniques for Measuring the Parameters of the Helix−Coil Transition in Peptides

21 June 2018

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Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol

21 June 2018

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Amino acid preferences for specific locations at the ends of alpha helices

21 June 2018

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Structure of ubiquitin refined at 1.8 A resolution

21 June 2018

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Helix signals in 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=3115786

Capping and alpha-helix stability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Unusually stable helix formation in short alanine-based peptides

21 June 2018

1 reference

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Calorimetric determination of the enthalpy change for the alpha-helix to coil transition of an alanine peptide in water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Dynamics of folded 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=3115786

Spin relaxation enhancement confirms dominance of extended conformations in short alanine peptides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Electron density redistribution accounts for half the cooperativity of alpha helix formation

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Temperature dependence of the thermodynamics of helix-coil transition

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Helix-coil transitions re-visited

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Elucidating the folding problem of helical peptides using empirical parameters

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Structure and Dynamics of the Homologous Series of Alanine Peptides: A Joint Molecular Dynamics/NMR Study

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3115786

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

31 October 2018

1 reference

12 December 2020

H-bonding cooperativity and energetics of alpha-helix formation of five 17-amino acid peptides

1 reference

12 December 2020

Folding kinetics of a naturally occurring helical peptide: implication of the folding speed limit of helical proteins

1 reference

12 December 2020

Self-Consistency Analysis of Dipolar Couplings in Multiple Alignments of Ubiquitin

1 reference

12 December 2020

Intermolecular potentials

1 reference

12 December 2020

Refinement of protein conformations using a macromolecular energy minimization procedure

1 reference

12 December 2020

Identifiers

DOI

10.1021/JP901540T

1 reference

27 July 2017

1 reference

27 July 2017

1 reference