(Q34428445)

2 August 2017

title

Computational study of unfolding and regulation mechanism of preQ1 riboswitches (English)

1 reference

2 August 2017

Zhou Gong

1

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2 August 2017

Yunjie Zhao

series ordinal

2

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2 August 2017

Changjun Chen

series ordinal

3

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2 August 2017

Yi Xiao

series ordinal

4

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2 August 2017

language of work or name

English

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publication date

17 September 2012

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2 August 2017

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2 August 2017

volume

7

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2 August 2017

issue

9

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2 August 2017

page(s)

e45239

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Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

17 September 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Riboswitch structure in the ligand-free state

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

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

6 July 2018

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

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Comparison of solution and crystal structures of preQ1 riboswitch reveals calcium-induced changes in conformation and dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Cooperative and directional folding of the preQ1 riboswitch aptamer domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Riboswitches and the RNA world

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Loop and stem dynamics during RNA hairpin folding and unfolding

6 July 2018

1 reference

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Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Folding of a transcriptionally acting preQ1 riboswitch

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Determination of riboswitch structures: light at the end of the tunnel?

6 July 2018

1 reference

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Structural Insights into riboswitch control of the biosynthesis of queuosine, a modified nucleotide found in the anticodon of tRNA

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

The distributions, mechanisms, and structures of metabolite-binding riboswitches

6 July 2018

1 reference

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Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

6 July 2018

1 reference

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Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

6 July 2018

1 reference

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UCSF Chimera--a visualization system for exploratory research and analysis

6 July 2018

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Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

"New view" of protein folding reconciled with the old through multiple unfolding simulations.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

VMD: visual molecular dynamics

6 July 2018

1 reference

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Protein unfolding pathways explored through molecular dynamics simulations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Simulations of protein folding and unfolding

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3444477

Theory and applications of the generalized Born solvation model in macromolecular simulations

27 October 2018

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12 December 2020

The dynamic nature of RNA as key to understanding riboswitch mechanisms

1 reference

12 December 2020

Improvements of the hierarchical approach for predicting RNA tertiary structure

1 reference

12 December 2020

Is protein unfolding the reverse of protein folding? A lattice simulation analysis

1 reference

12 December 2020

Atomistic analysis of pseudoknotted RNA unfolding

1 reference

12 December 2020

RNA stability under different combinations of amber force fields and solvation models

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0045239

Identifiers

DOI

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2 August 2017

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2 August 2017

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