High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations (Q27014673)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24043821%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

title

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations (English)

1 reference

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molecular dynamics simulation

22 February 2020

main subject

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author

Alan A Chen

series ordinal

1

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22 February 2020

2

Angel E García

1 reference

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22 February 2020

language of work or name

1 reference

16 September 2013

1 reference

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22 February 2020

number of pages

6

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Proceedings of the National Academy of Sciences of the United States of America

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published in

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22 February 2020

volume

110

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22 February 2020

issue

42

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22 February 2020

page(s)

16820-16825

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describes a project that uses

22 February 2020

molecular dynamics simulation

1 reference

Mfold web server for nucleic acid folding and hybridization prediction

inferred from title

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3801082

Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops"

21 March 2017

1 reference

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High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

21 March 2017

1 reference

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The crystal structure of UUCG tetraloop

21 March 2017

1 reference

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A network of heterogeneous hydrogen bonds in GNRA tetraloops

21 March 2017

1 reference

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Solution Structure of the CUUG Hairpin Loop: A Novel RNA Tetraloop Motif

21 March 2017

1 reference

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Structure of the 70S ribosome complexed with mRNA and tRNA

21 March 2017

1 reference

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

21 March 2017

1 reference

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Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

7 April 2017

1 reference

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Computer Folding of RNA Tetraloops? Are We There Yet?

28 September 2017

1 reference

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How fast-folding proteins fold

28 September 2017

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Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

28 September 2017

1 reference

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Four small puzzles that Rosetta doesn't solve

28 September 2017

1 reference

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

28 September 2017

1 reference

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Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe

28 September 2017

1 reference

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Does water play a structural role in the folding of small nucleic acids?

28 September 2017

1 reference

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Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3801082

Dynamics of the RNA hairpin GNRA tetraloop

28 September 2017

1 reference

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28 September 2017

1 reference

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Structural Features that Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops

28 September 2017

1 reference

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Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling

28 September 2017

1 reference

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Structural insight into RNA hairpin folding intermediates

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3801082

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates

31 May 2018

1 reference

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

31 May 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1309392110

RNA tetraloop folding reveals tension between backbone restraints and molecular interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1309392110

Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1309392110

Folding of a small RNA hairpin based on simulation with replica exchange molecular dynamics.

21 January 2018

1 reference

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On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes.

21 January 2018

1 reference

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Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

21 January 2018

1 reference

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Free energy calculations for DNA base stacking by replica-exchange umbrella sampling

21 January 2018

1 reference

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21 January 2018

Stacking interactions

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1309392110

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

21 January 2018

1 reference

12 December 2020

Direct revelation of multiple conformations in RNA by femtosecond dynamics

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12 December 2020

Nanosecond relaxation processes in aqueous mononucleoside solutions

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12 December 2020

Exploring the energy landscape of a small RNA hairpin

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12 December 2020

The interaction of nucleosides in aqueous solution

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12 December 2020

Molecular Dynamics Simulation of the Structure, Dynamics, and Thermostability of the RNA Hairpins uCACGg and cUUCGg

1 reference

12 December 2020

Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation

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12 December 2020

Identifiers

DOI

10.1073/PNAS.1309392110

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24043821%20AND%20SRC:MED&resulttype=core&format=json

22 February 2020

ADS bibcode

2013PNAS..11016820C

0 references

1 reference

2 references

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22 February 2020

2 references