(Q30378249)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

title

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

0 references

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

Pengyu Ren

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

author name string

Johnny C Wu

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

David P Gardner

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

Stuart Ozer

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

language of work or name

English

0 references

publication date

18 June 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

Journal of Molecular Biology

31 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

volume

391

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

page(s)

769-783

1 reference

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describes a project that uses

31 January 2020

SQL

1 reference

26 June 2022

https://europepmc.org/article/PMC/PMC2778063

inferred from PubMed Central ID database lookup

cites work

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1 reference

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20 June 2018

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20 June 2018

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The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Automated de novo prediction of native-like RNA tertiary structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Statistical potential for assessment and prediction of protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

CONTRAfold: RNA secondary structure prediction without physics-based models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

The UAA/GAN internal loop motif: a new RNA structural element that forms a cross-strand AAA stack and long-range tertiary interactions

20 June 2018

1 reference

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Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.

20 June 2018

1 reference

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Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Describing RNA structure by libraries of clustered nucleotide doublets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Stacked-unstacked equilibrium at the nick site of DNA

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

STRUCTURE OF A RIBONUCLEIC ACID

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Pfold: RNA secondary structure prediction using stochastic context-free grammars

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

The solution structure of the loop E region of the 5S rRNA from spinach chloroplasts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Specificity of RNA-RNA helix recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

The accuracy of ribosomal RNA comparative structure models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

RNA secondary structure prediction using stochastic context-free grammars and evolutionary history

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

RNA tertiary structure mediation by adenosine platforms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

The conformation of loop E of eukaryotic 5S ribosomal RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

A major family of motifs involving G.A mismatches in ribosomal RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Stochastic context-free grammars for tRNA modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Frequent use of the same tertiary motif by self-folding RNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

RNA hairpin loop stability depends on closing base pair

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Involvement of a GNRA tetraloop in long-range RNA tertiary interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Secondary structure model for 23S ribosomal RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Comparison of fungal mitochondrial introns reveals extensive homologies in RNA secondary structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast 23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Detailed molecular model for transfer ribonucleic acid

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Comparative anatomy of 16-S-like ribosomal RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Comparative and functional anatomy of group II catalytic introns--a review

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Higher order structural elements in ribosomal RNAs: pseudo-knots and the use of noncanonical pairs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

The secondary structure of ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2778063

Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA

26 November 2018

1 reference

12 December 2020

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

1 reference

12 December 2020

The lonepair triloop: a new motif in RNA structure

1 reference

12 December 2020

Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs

1 reference

12 December 2020

The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: a statistical model for nonbonded interactions

1 reference

12 December 2020

The stability and structure of tandem GA mismatches in RNA depend on closing base pairs

1 reference

12 December 2020

Predicting U-turns in ribosomal RNA with comparative sequence analysis

1 reference

12 December 2020

Why do protein architectures have Boltzmann-like statistics?

1 reference

12 December 2020

[Secondary and topographic structure of ribosomal RNA 16S of Escherichia coli]

1 reference

12 December 2020

5S RNA secondary structure

1 reference

12 December 2020

Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs

1 reference

12 December 2020

A story: unpaired adenosine bases in ribosomal RNAs

1 reference

12 December 2020

10.1016/J.JMB.2009.06.036

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19540243%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

PubMed publication ID

19540243

1 reference