(Q33687577)

28 July 2017

title

Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly (English)

1 reference

28 July 2017

Experimental Verification of Force Fields for Molecular Dynamics Simulations Using Gly-Pro-Gly-Gly (English)

1 reference

9 July 2024

author

‪Denis Courtier-Murias

2

object named as

Denis Courtier-Murias

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20825228

reference URL

9 July 2024

author name string

Abil E. Aliev

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20825228

reference URL

9 July 2024

language of work or name

English

0 references

publication date

1 September 2010

1 reference

28 July 2017

30 September 2010

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=20825228

reference URL

full work available at URL

9 July 2024

number of pages

18

1 reference

based on heuristic

inferred from page(s)

https://pubs.acs.org/doi/pdf/10.1021/jp101581h

1 reference

Journal of Physical Chemistry B

9 July 2024

published in

1 reference

28 July 2017

volume

114

1 reference

28 July 2017

issue

38

1 reference

28 July 2017

page(s)

12358-12375

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A combined NMR/MD/QM approach for structure and dynamics elucidations in the solution state: pilot studies using tetrapeptides

28 July 2017

cites work

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Modern protein force fields behave comparably in molecular dynamics simulations

9 July 2024

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Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

9 July 2024

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9 July 2024

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Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models

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Force Field Modeling of Amino Acid Conformational Energies

9 July 2024

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A consensus view of protein dynamics

9 July 2024

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

9 July 2024

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Are current molecular dynamics force fields too helical?

9 July 2024

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Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation

9 July 2024

11

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Evaluating the performance of the ff99SB force field based on NMR scalar coupling data

9 July 2024

12

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Are current semiempirical methods better than force fields? A study from the thermodynamics perspective.

9 July 2024

13

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Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.

9 July 2024

14

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Proline cis-trans isomerization and protein folding

9 July 2024

16

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A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

9 July 2024

18

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Solid-state NMR studies of collagen-based parchments and gelatin

9 July 2024

19

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Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule

9 July 2024

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Parametrization of aliphatic CHn united atoms of GROMOS96 force field

9 July 2024

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A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

9 July 2024

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

9 July 2024

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

9 July 2024

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

9 July 2024

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Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

9 July 2024

28

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

9 July 2024

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

9 July 2024

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Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids

9 July 2024

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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

9 July 2024

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Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models.

9 July 2024

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The relationship between proton-proton NMR coupling constants and substituent electronegativities—I

9 July 2024

36

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On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol

9 July 2024

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

9 July 2024

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A smooth particle mesh Ewald method

9 July 2024

48

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A Leap-frog Algorithm for Stochastic Dynamics

9 July 2024

50

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Canonical sampling through velocity rescaling

9 July 2024

51

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Polymorphic transitions in single crystals: A new molecular dynamics method

9 July 2024

52

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Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles

9 July 2024

54

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Probing multiple effects on 15N, 13C alpha, 13C beta, and 13C' chemical shifts in peptides using density functional theory

9 July 2024

56

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Empirical Comparisons of Models for Chemical-Shift Calculation in Proteins

9 July 2024

57

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Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin

9 July 2024

58

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Structure of ubiquitin refined at 1.8 A resolution

9 July 2024

59

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Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

9 July 2024

61

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Conformations of amino acids in proteins.

9 July 2024

64

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Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

9 July 2024

67

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Force fields for protein simulations

9 July 2024

68

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Comparison of protein force fields for molecular dynamics simulations

9 July 2024

69

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Conformational transition states of a beta-hairpin peptide between the ordered and disordered conformations in explicit water

9 July 2024

71

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The missing term in effective pair potentials

9 July 2024

73

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Comparison of simple potential functions for simulating liquid water

9 July 2024

74

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Temperature and size dependence for Monte Carlo simulations of TIP4P water

9 July 2024

75

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A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

9 July 2024

76

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What ice can teach us about water interactions: a critical comparison of the performance of different water models.

9 July 2024

78

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Quantum mechanical and NMR studies of ring puckering and cis/trans-rotameric interconversion in prolines and hydroxyprolines

9 July 2024

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Stereochemical criteria for polypeptide and protein chain conformations. II. Allowed conformations for a pair of peptide units

9 July 2024

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9 July 2024

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248

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Maccallum P. H.

1995

1 reference

The Ramachandran plots of glycine and pre-proline

9 July 2024

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The quantum-chemical calculation of NMR indirect spin–spin coupling constants

9 July 2024

84

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Theoretical Karplus relationships for vicinal coupling constants around χ1 in Valine

9 July 2024

85

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Assessment of Density Functionals for Predicting One-Bond Carbon-Hydrogen NMR Spin-Spin Coupling Constants

9 July 2024

86

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Conformational analysis of L-prolines in water

9 July 2024

89

1 reference

Proline zwitterion dynamics in solution, glass, and crystalline state

9 July 2024

90

1 reference

Comparison of quantitative conformer analyses by nuclear magnetic resonance and Raman optical activity spectra for model dipeptides.

9 July 2024

91

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Conformational preferences of non-prolyl and prolyl residues.

9 July 2024

92

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Puckering Transition of Proline Residue in Water

9 July 2024

93

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Highly stable cyclic dimers based on non-covalent interactions

9 July 2024

94

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Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

9 July 2024

95

1 reference

9 July 2024

Identifiers

DOI

10.1021/JP101581H

1 reference

28 July 2017

1 reference