Accurate SHAPE-directed RNA structure determination (Q24646758)

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Tian W Li

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David H Mathews

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Kevin M Weeks

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

4

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language of work or name

English

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publication date

6 January 2009

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number of pages

6

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based on heuristic

inferred from page(s)

published in

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volume

106

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issue

1

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page(s)

97-102

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cites work

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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

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Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

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Structure of the 30S ribosomal subunit

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CONTRAfold: RNA secondary structure prediction without physics-based models

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Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution

7 April 2017

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RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

7 April 2017

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Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

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SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA.

27 September 2017

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Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms

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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

27 September 2017

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RNA secondary structure prediction

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Efficient siRNA selection using hybridization thermodynamics

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A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry

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SECONDARY STRUCTURE IN RIBONUCLEIC ACIDS.

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Regulation of translation via mRNA structure in prokaryotes and eukaryotes

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Extracting stacking interaction parameters for RNA from the data set of native structures

27 September 2017

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The accuracy of ribosomal RNA comparative structure models

27 September 2017

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No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

27 September 2017

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Thermodynamics of base pairing

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Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA

27 September 2017

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Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

30 May 2018

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Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops

21 January 2018

1 reference

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RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0806929106

Complex ligand-induced conformational changes in tRNA(Asp) revealed by single-nucleotide resolution SHAPE chemistry

21 January 2018

1 reference

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Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19109441

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A collapsed non-native RNA folding state

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19109441

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0806929106

1 reference

1121068

ADS bibcode

2009PNAS..106...97D

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1121068

1 reference

1 reference

1 reference