(Q27676633)

English

A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations (English)

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

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molecular dynamics simulation

0 references

George C. Schatz

4

object named as

George C Schatz

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

author name string

Ilyas Yildirim

1

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

HaJeung Park

2

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

Matthew D Disney

3

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

language of work or name

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publication date

26 February 2013

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Europe PubMed Central

PubMed publication ID

24 June 2017

Journal of the American Chemical Society

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Europe PubMed Central

PubMed publication ID

24 June 2017

135

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

9

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

3528-3538

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

NMR spectroscopy and molecular dynamics simulation of r(CCGCUGCGG)₂ reveal a dynamic UU internal loop found in myotonic dystrophy type 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Structural basis for hygromycin B inhibition of protein biosynthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

A Steric Block in Translation Caused by the Antibiotic Spectinomycin

1 reference

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20 March 2017

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

The free energy landscape of small peptides as obtained from metadynamics with umbrella sampling corrections

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Abnormal gene product identified in hereditary dentatorubral-pallidoluysian atrophy (DRPLA) brain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Structures of the bacterial ribosome at 3.5 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Likelihood-enhanced fast rotation functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

PHENIX: building new software for automated crystallographic structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

RNA toxicity is a component of ataxin-3 degeneration in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Huntington's disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Characterization and localization of the FMR-1 gene product associated with fragile X syndrome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

20 March 2017

Trinucleotide Repeat Disorders

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

7 April 2017

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

7 April 2017

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Design of a bioactive small molecule that targets the myotonic dystrophy type 1 RNA via an RNA motif-ligand database and chemical similarity searching

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Chemical correction of pre-mRNA splicing defects associated with sequestration of muscleblind-like 1 protein by expanded r(CAG)-containing transcripts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

CAG repeats mimic CUG repeats in the misregulation of alternative splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Milestones in ataxia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Milestones in huntington disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Non-ATG-initiated translation directed by microsatellite expansions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Structural characterization of naturally occurring RNA single mismatches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Positional and Neighboring Base Pair Effects on the Thermodynamic Stability of RNA Single Mismatches

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Roles of trinucleotide-repeat RNA in neurological disease and degeneration.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Sam68 sequestration and partial loss of function are associated with splicing alterations in FXTAS patients

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Structural diversity of triplet repeat RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Rational design of ligands targeting triplet repeating transcripts that cause RNA dominant disease: application to myotonic muscular dystrophy type 1 and spinocerebellar ataxia type 3.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Allele-specific silencing of mutant huntingtin and ataxin-3 genes by targeting expanded CAG repeats in mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Long-timescale molecular dynamics simulations of protein structure and function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Pur alpha binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Structure of the ribosome-bound cricket paralysis virus IRES RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Structural basis for mRNA and tRNA positioning on the ribosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Structural analysis of kasugamycin inhibition of translation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Computational approaches for investigating base flipping in oligonucleotides

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

The structural basis of myotonic dystrophy from the crystal structure of CUG repeats

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Towards an accurate representation of electrostatics in classical force fields: efficient implementation of multipolar interactions in biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Simulation and modeling of nucleic acid structure, dynamics and interactions

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Theoretical methods for the simulation of nucleic acids.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Simulations of nucleic acids and their complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Nucleic acids: theory and computer simulation, Y2K.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

29 September 2017

Benchmarking AMBER force fields for RNA: comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

2 June 2018

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

2 June 2018

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

2 June 2018

A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

2 June 2018

A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

2 June 2018

Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings.

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

27 November 2018

Thermodynamic characterization of single mismatches found in naturally occurring RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

27 November 2018

Neuropathology of fragile X-associated tremor/ataxia syndrome (FXTAS).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

27 November 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

27 November 2018

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3625063

27 November 2018

The muscular dystrophies

1 reference

https://pubmed.ncbi.nlm.nih.gov/23441937

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Calculation of free energy through successive umbrella sampling

1 reference

https://pubmed.ncbi.nlm.nih.gov/23441937

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Exploring the Essential Dynamics of B-DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/23441937

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Processing of X-ray diffraction data collected in oscillation mode

1 reference

https://pubmed.ncbi.nlm.nih.gov/23441937

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Trinucleotide repeat expansion and human disease

1 reference

https://pubmed.ncbi.nlm.nih.gov/23441937

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1021/JA3108627

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

24 June 2017

ResearchGate publication ID

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