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Computational analysis of RNA structures with chemical probing data
scientific article
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scholarly article
1 reference
stated in
Europe PubMed Central
PMC publication ID
4437859
retrieved
24 September 2017
review article
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stated in
Europe PubMed Central
title
Computational analysis of RNA structures with chemical probing data
(English)
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stated in
Europe PubMed Central
PMC publication ID
4437859
retrieved
24 September 2017
main subject
RNA analysis
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based on heuristic
inferred from title
author
Shaojie Zhang
series ordinal
2
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stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
author name string
Ping Ge
series ordinal
1
1 reference
stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
language of work or name
English
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inferred from title
publication date
14 February 2015
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Europe PubMed Central
PMC publication ID
4437859
retrieved
24 September 2017
published in
Methods
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Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
volume
79-80
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stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
page(s)
60-66
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Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
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Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution
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Local similarity in RNA secondary structures.
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RNA structure: reading the ribosome
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Fast and reliable prediction of noncoding RNAs
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Crystallization of RNA and RNA-protein complexes
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
MicroRNAs: small RNAs with a big role in gene regulation
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
A statistical sampling algorithm for RNA secondary structure prediction
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
RSEARCH: finding homologs of single structured RNA sequences
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Development of hammerhead ribozymes to modulate endogenous gene expression for functional studies.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Secondary structure prediction for aligned RNA sequences
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Correlating structural dynamics and function in single ribozyme molecules
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
An expanding universe of noncoding RNAs
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Noncoding RNA gene detection using comparative sequence analysis
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Non–coding RNA genes and the modern RNA world
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
RNA pseudoknot prediction in energy-based models
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Discrete molecular dynamics studies of the folding of a protein-like model.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA.Fe(II) at position 47
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Protection of ribosomal RNA from kethoxal in polyribosomes. Implication of specific sites in ribosome function
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Identification by RNA-protein cross-linking of ribosomal proteins located at the interface between the small and the large subunits of mammalian ribosomes
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Chemical probes for higher-order structure in RNA
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase
1 reference
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reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Improved predictions of secondary structures for RNA
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Probing the structure of RNAs in solution
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
Pseudoknots: a new motif in the RNA game
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
RNA substrate binding site in the catalytic core of the Tetrahymena ribozyme
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
All oxygens in nucleic acids react with carcinogenic ethylating agents
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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21 June 2018
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
HiTRACE: high-throughput robust analysis for capillary electrophoresis
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
FastR: fast database search tool for non-coding RNA.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Simple but predictive protein models
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNA(Asp) transcripts
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Untying the FIV frameshifting pseudoknot structure by MS3D.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Conserved RNA secondary structures in viral genomes: a survey.
1 reference
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
retrieved
25 November 2018
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4437859
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25 November 2018
Fast folding and comparison of RNA secondary structures
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7 January 2021
A guide for probing native small nuclear RNA and ribonucleoprotein structures
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7 January 2021
Comparison of transfer ribonucleic acid structures using cobra venom and S1 endonucleases
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7 January 2021
Structural Analysis of a Group II Intron by Chemical Modifications and Minimal Energy Calculations
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7 January 2021
One sequence, two ribozymes: implications for the emergence of new ribozyme folds
1 reference
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Crossref
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7 January 2021
Identifiers
DOI
10.1016/J.YMETH.2015.02.003
1 reference
stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
PMC publication ID
4437859
1 reference
stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
PubMed publication ID
25687190
1 reference
stated in
Europe PubMed Central
PMC publication ID
4437859
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25687190%20AND%20SRC:MED&resulttype=core&format=json
retrieved
3 June 2020
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