Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization (Q24540294)

PubMed publication ID

15272118

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

27 April 2024

language of work or name

English

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publication date

August 2004

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1178-90

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

A statistical sampling algorithm for RNA secondary structure prediction

24 March 2017

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

24 March 2017

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Initial sequencing and analysis of the human genome

24 March 2017

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Design of multistable RNA molecules

24 March 2017

1 reference

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Predicting oligonucleotide affinity to nucleic acid targets

24 March 2017

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The Ribonuclease P Database

24 March 2017

1 reference

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Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Initial sequencing and comparative analysis of the mouse genome

24 March 2017

1 reference

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Non–coding RNA genes and the modern RNA world

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The Sequence of the Human Genome

24 March 2017

1 reference

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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

24 March 2017

1 reference

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NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structural insights into peptide bond formation

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structure of the 30S ribosomal subunit

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The structural basis of ribosome activity in peptide bond synthesis

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Three-dimensional folding of an RNA hairpin required for packaging HIV-1

24 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Identification of novel genes coding for small expressed RNAs

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The genome sequence of Drosophila melanogaster

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Genome sequence of the nematode C. elegans: a platform for investigating biology

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Vienna RNA secondary structure server

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

A dynamic programming algorithm for RNA structure prediction including pseudoknots

24 March 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

24 March 2017

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Signal recognition particle contains a 7S RNA essential for protein translocation across the endoplasmic reticulum

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The equilibrium partition function and base pair binding probabilities for RNA secondary structure

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

On finding all suboptimal foldings of an RNA molecule

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Compilation of tRNA sequences and sequences of tRNA genes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Thermodynamic criteria for high hit rate antisense oligonucleotide design

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The accuracy of ribosomal RNA comparative structure models

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

The chemical repertoire of natural ribozymes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

SRPDB (Signal Recognition Particle Database).

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Microbial genome sequencing

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

5S ribosomal RNA database Y2K

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Differential chemical probing of a group II self-splicing intron identifies bases involved in tertiary interactions and supports an alternative secondary structure model of domain V

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Using reliability information to annotate RNA secondary structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Thermodynamics of coaxially stacked helixes with GA and CC mismatches

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

"Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Analysis of the structure of Tetrahymena nuclear RNAs in vivo: telomerase RNA, the self-splicing rRNA intron, and U2 snRNA.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structural analyses of E.coli 5S RNA fragments, their associates and complexes with proteins L18 and L25

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Probing the structure of RNAs in solution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

A conserved pseudoknot in telomerase RNA

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Changes in 7SL RNA conformation during the signal recognition particle cycle

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structlre of transfer RNA molecules containing the long variable loop

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Complete suboptimal folding of RNA and the stability of secondary structures.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Assessing the reliability of RNA folding using statistical mechanics

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Viroid processing: switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

A conserved secondary structure for telomerase RNA

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structure-sensitive RNA footprinting of yeast nuclear ribonuclease P.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Structure and accessibility of domain I of Escherichia coli 23 S RNA in free RNA, in the L24-RNA complex and in 50 S subunits. Implications for ribosomal assembly.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16S ribosomal RNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

19 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

A partition function algorithm for nucleic acid secondary structure including pseudoknots

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Differential helix stabilities and sites pre-organized for tertiary interactions revealed by monitoring local nucleotide flexibility in the bI5 group I intron RNA.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Prediction of RNA base pairing probabilities on massively parallel computers.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

Fast evaluation of internal loops in RNA secondary structure prediction.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1370608

One sequence, two ribozymes: implications for the emergence of new ribozyme folds

29 November 2018

1 reference

12 December 2020

Enzymatic approaches to probing of RNA secondary and tertiary structure

1 reference

12 December 2020

Structural Analysis of a Group II Intron by Chemical Modifications and Minimal Energy Calculations

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

The Signal Recognition Particle Database (SRPDB)

1 reference

12 December 2020

Thermodynamics of three-way multibranch loops in RNA

1 reference

12 December 2020

Chemical modification of guanine residues of mouse 5 S ribosomal RNA with kethoxal. (Nucleosides and nucleotides 46)

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1261/RNA.7650904

1 reference

release_alvaqunlkff4hnjp23iykdn5hi

Fatcat ID

0 references

1 reference

1 reference

PubMed publication ID

15272118

1 reference