Time-averaged order parameter restraints in molecular dynamics simulations (Q50775844)

19 March 2018

title

Time-averaged order parameter restraints in molecular dynamics simulations (English)

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19 March 2018

author

Niels Hansen

1

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19 March 2018

Wilfred F van Gunsteren

4

object named as

Wilfred F van Gunsteren

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19 March 2018

author name string

Fabian Heller

2

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19 March 2018

Nathan Schmid

3

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19 March 2018

publication date

14 October 2014

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19 March 2018

Journal of Biomolecular NMR

published in

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19 March 2018

volume

60

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19 March 2018

issue

2-3

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19 March 2018

page(s)

169-187

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19 March 2018

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

cites work

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Determination of protein structures consistent with NMR order parameters

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Theory for nuclear magnetic relaxation of probes in anisotropic systems: application of cholesterol in phospholipid vesicles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Combined use of proton-proton overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

The GROMOS software for biomolecular simulation: GROMOS05.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Biomolecular structure refinement based on adaptive restraints using local-elevation simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

GROMOS Software for the Analysis of Biomolecular Simulation Trajectories

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Optimal superpositioning of flexible molecule ensembles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Interpreting experimental data by using molecular simulation instead of model building

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

How noise in force fields can affect the structural refinement of protein models?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Orientation restraints in molecular dynamics simulations using time and ensemble averaging

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

On the nature of molecular conformations inferred from high-resolution NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Separability between overall and internal motion: a protein folding problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Sampling bottlenecks in de novo protein structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Improved treatment of the protein backbone in empirical force fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Molecular dynamics study of calbindin D9k in the apo and singly and doubly calcium-loaded states

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Progress and challenges in high-resolution refinement of protein structure models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Parametrisation of time-averaged distance restraints in MD simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Probabilistic Determination of Native State Ensembles of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

On the Use of Experimental Observations to Bias Simulated Ensembles

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Using NMR to study fast dynamics in proteins: methods and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Biomolecular structure refinement using the GROMOS simulation software

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Molecular dynamics with weighted time-averaged restraints for a DNA octamer. Dynamic interpretation of nuclear magnetic resonance data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

On using time-averaging restraints in molecular dynamics simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Comparison of MD Simulations and NMR Experiments for Hen Lysozyme. Analysis of Local Fluctuations, Cooperative Motions, and Global Changes

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Internal mobility of the basic pancreatic trypsin inhibitor in solution: a comparison of NMR spin relaxation measurements and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Structure refinement using time-averaged J-coupling constant restraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Molecular simulation as an aid to experimentalists.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Evaluating rotational diffusion from protein MD simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

SWARM-MD: Searching Conformational Space by Cooperative Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

The use of model selection in the model-free analysis of protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Multidimensional replica-exchange method for free-energy calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Peptide folding simulations: no solvent required?

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

A Multifaceted Approach to the Interpretation of NMR Order Parameters: A Case Study of a Dynamic α-Helix†

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1007/S10858-014-9866-7

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

21 January 2018

1 reference

12 December 2020

How is an NMR structure best defined? An analysis of molecular dynamics distance-based approaches

1 reference

12 December 2020

Inference of structure ensembles of flexible biomolecules from sparse, averaged data

1 reference

12 December 2020

Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data

1 reference

12 December 2020

The combined use of NMR, distance geometry, and restrained molecular dynamics for the conformational study of a cyclic somatostatin analogue

1 reference

12 December 2020

Refinement of protein structure homology models via long, all-atom molecular dynamics simulations

1 reference

12 December 2020

Backbone dynamics and energetics of a calmodulin domain mutant exchanging between closed and open conformations

1 reference

12 December 2020

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

1 reference

12 December 2020

How well do time-averaged J-coupling restraints work?

1 reference

12 December 2020

Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

1 reference

12 December 2020

Accessibility and order of water sites in and around proteins: A crystallographic time-averaging study

1 reference

12 December 2020

Time-averaging crystallographic refinement: possibilities and limitations using alpha-cyclodextrin as a test system

1 reference

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10.1007/S10858-014-9866-7

Identifiers

DOI

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19 March 2018

1 reference

19 March 2018