RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case (Q31062836)

28 June 2017

title

RNA unrestrained molecular dynamics ensemble improves agreement with experimental NMR data compared to single static structure: a test case (English)

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molecular dynamics simulation

28 June 2017

main subject

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author name string

Robert A Beckman

1

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28 June 2017

David Moreland

2

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28 June 2017

Shirley Louise-May

3

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28 June 2017

Christine Humblet

4

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28 June 2017

publication date

1 May 2006

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Journal of Computer - Aided Molecular Design

28 June 2017

published in

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28 June 2017

volume

20

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28 June 2017

issue

5

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28 June 2017

page(s)

263-279

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Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

28 June 2017

cites work

1 reference

Crossref

https://api.crossref.org/works/10.1007%2FS10822-006-9049-Z

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

21 January 2018

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The effect of motional averaging on the calculation of NMR-derived structural properties

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The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage

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Formation of a stable triplex from a single DNA strand

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Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy

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Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor

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The linkage between magnesium binding and RNA folding.

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Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme

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Molecular dynamics studies of U1A-RNA complexes

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Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach

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Atomic-level accuracy in simulations of large protein crystals

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The detailed structure of tandem G.A mismatched base-pair motifs in RNA duplexes is context dependent

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Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat

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Toward a Dynamical Structure of DNA: Comparison of Theoretical and Experimental NOE Intensities

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Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease

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Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding

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Fast internal main-chain dynamics of human ubiquitin

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A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing

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Parameters for the calculation of proton NMR chemical shifts of oligoribonucleotides

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Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy

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The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations

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Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides

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Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA

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Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.

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A molecular dynamics study of the bis-intercalation complexes of echinomycin with d(ACGT)2 and d(TCGA)2: rationale for sequence-specific Hoogsteen base pairing

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12 December 2020

Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations

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12 December 2020

Three-dimensional structure of a hammerhead ribozyme

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12 December 2020

Assignment of the 31P and 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy

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12 December 2020

Base dynamics in a UUCG tetraloop RNA hairpin characterized by 15N spin relaxation: correlations with structure and stability

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12 December 2020

Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

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12 December 2020

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA

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12 December 2020

10.1007/S10822-006-9049-Z

Identifiers

DOI

1 reference

journals/jcamd/BeckmanMLH06

28 June 2017

DBLP publication ID

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DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1025819944

0 references

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