(Q30986204)

28 June 2017

title

Validation of the 53A6 GROMOS force field (English)

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28 June 2017

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1

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28 June 2017

Wilfred F van Gunsteren

series ordinal

4

object named as

Wilfred F van Gunsteren

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28 June 2017

Thereza A Soares

2

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author name string

Nico F A van der Vegt

series ordinal

3

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28 June 2017

publication date

1 April 2005

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European Biophysics Journal

28 June 2017

published in

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28 June 2017

volume

34

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28 June 2017

issue

4

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28 June 2017

page(s)

273-284

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Molecular dynamics simulation of nucleic acids

28 June 2017

cites work

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12 December 2020

Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field

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Molecular dynamics simulation of nucleic acids: successes, limitations, and promise

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12 December 2020

The Key to Solving the Protein-Folding Problem Lies in an Accurate Description of the Denatured State Financial support from the Schweizerischer Nationalfonds (Project no. 21-50929.97) is gratefully acknowledged

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Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain

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The B-DNA dodecamer at high resolution reveals a spine of water on sodium

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Unfolded state of peptides

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Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance

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A new GROMOS force field for hexopyranose-based carbohydrates

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Structural Determinants of Protein Dynamics: Analysis of 15N NMR Relaxation Measurements for Main-Chain and Side-Chain Nuclei of Hen Egg White Lysozyme

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Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data

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Assessment of the molecular dynamics structure of DNA in solution based on calculated and observed NMR NOESY volumes and dihedral angles from scalar coupling constants

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12 December 2020

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

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Ligand binding affinity prediction by linear interaction energy methods

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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

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12 December 2020

Structure of a B-DNA dodecamer. III. Geometry of hydration

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12 December 2020

Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes

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Structure of a B-DNA dodecamer: conformation and dynamics

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Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.

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A standard reference frame for the description of nucleic acid base-pair geometry.

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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

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A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

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Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: a molecular dynamics simulation study

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12 December 2020

Analysis of .vphi. and .chi.1 torsion angles for hen lysozyme in solution from proton NMR spin-spin coupling constants

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

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High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission

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Molecular dynamics simulations of human alpha-lactalbumin: changes to the structural and dynamical properties of the protein at low pH.

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Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

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Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

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12 December 2020

Side-chain conformational disorder in a molten globule: molecular dynamics simulations of the A-state of human alpha-lactalbumin

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12 December 2020

Structure of Hen Lysozyme in Solution

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12 December 2020

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

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12 December 2020

Calculation of the free energy of solvation for neutral analogs of amino acid side chains

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Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

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Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

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Can One Derive the Conformational Preference of a β-Peptide from Its CD Spectrum?

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3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

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12 December 2020

Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

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Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures

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Folding-unfolding thermodynamics of a beta-heptapeptide from equilibrium simulations

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12 December 2020

An improved nucleic acid parameter set for the GROMOS force field

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12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

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12 December 2020

Refinement of homology-based protein structures by molecular dynamics simulation techniques

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12 December 2020

Water molecules in DNA recognition II: a molecular dynamics view of the structure and hydration of the trp operator

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12 December 2020

10.1007/S00249-004-0448-6

Identifiers

DOI

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28 June 2017

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