Evaluation of the information content of RNA structure mapping data for secondary structure prediction (Q33562602)

28 July 2017

title

Evaluation of the information content of RNA structure mapping data for secondary structure prediction (English)

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28 July 2017

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Scott Quarrier

1

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Alain Laederach

object named as

Alain Laederach

5

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author name string

Joshua S Martin

2

1 reference

28 July 2017

Lauren Davis-Neulander

3

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28 July 2017

Arthur Beauregard

4

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28 July 2017

language of work or name

English

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publication date

22 April 2010

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28 July 2017

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28 July 2017

volume

16

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28 July 2017

issue

6

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28 July 2017

page(s)

1108-1117

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Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA

28 July 2017

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21 June 2018

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21 June 2018

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21 June 2018

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NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon

21 June 2018

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High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

21 June 2018

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

21 June 2018

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21 June 2018

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DMS footprinting of structured RNAs and RNA-protein complexes

21 June 2018

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21 June 2018

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Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

21 June 2018

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Local RNA structural changes induced by crystallization are revealed by SHAPE

21 June 2018

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21 June 2018

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Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule

21 June 2018

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21 June 2018

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RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

21 June 2018

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21 June 2018

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SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments

21 June 2018

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Crystal structure of a phage Twort group I ribozyme-product complex

21 June 2018

1 reference

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Monovalent ion-mediated folding of the Tetrahymena thermophila ribozyme

21 June 2018

1 reference

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Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

21 June 2018

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21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Identifying kinetic barriers to mechanical unfolding of the T. thermophila ribozyme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

The non-Watson-Crick base pairs and their associated isostericity matrices

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Probing RNA structure and RNA-ligand complexes with chemical probes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

DNA sequencing by capillary electrophoresis (review).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Crystal structure of a group I ribozyme domain: principles of RNA packing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Mapping tRNA structure in solution using double-strand-specific ribonuclease V1 from cobra venom

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

RNA structure analysis using T2 ribonuclease: detection of pH and metal ion induced conformational changes in yeast tRNAPhe

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Defining the inside and outside of a catalytic RNA molecule

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Probing the structure of RNAs in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Mapping adenines, guanines, and pyrimidines in RNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Monitoring structural changes in nucleic acids with single residue spatial and millisecond time resolution by quantitative hydroxyl radical footprinting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Computing the partition function and sampling for saturated secondary structures of RNA, with respect to the Turner energy model.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Local RNA base pairing probabilities in large sequences.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2874162

The Nucleic Acid Database

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20413617

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.1988510

1 reference

28 July 2017

1 reference

28 July 2017

1 reference