(Q35127973)

6 August 2017

title

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation (English)

1 reference

nearest neighbour algorithm

6 August 2017

0 references

1 reference

2

Douglas H Turner

1 reference

6 August 2017

Zhi John Lu

1

1 reference

6 August 2017

David H Mathews

series ordinal

3

1 reference

6 August 2017

language of work or name

English

0 references

publication date

18 September 2006

1 reference

6 August 2017

published in

Nucleic Acids Research

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6 August 2017

volume

34

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6 August 2017

issue

17

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6 August 2017

page(s)

4912-4924

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Uracil content of 16S rRNA of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures

6 August 2017

cites work

1 reference

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Predicting a set of minimal free energy RNA secondary structures common to two sequences

13 July 2018

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A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation

13 July 2018

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

13 July 2018

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RNA folding and unfolding

13 July 2018

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Salt-dependent heat capacity changes for RNA duplex formation

13 July 2018

1 reference

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Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme.

13 July 2018

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

13 July 2018

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The microRNA world: small is mighty

13 July 2018

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13 July 2018

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RNAsoft: A suite of RNA secondary structure prediction and design software tools

13 July 2018

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13 July 2018

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Molecular recognition in purine-rich internal loops: thermodynamic, structural, and dynamic consequences of purine for adenine substitutions in 5'(rGGCAAGCCU)2

13 July 2018

1 reference

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Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions

13 July 2018

1 reference

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The chemical repertoire of natural ribozymes

13 July 2018

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

13 July 2018

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Identification of novel genes coding for small expressed RNAs

13 July 2018

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On the stability of double stranded nucleic acids

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Recent insights on RNA folding mechanisms from catalytic RNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

A test of the model to predict unusually stable RNA hairpin loop stability

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

The ribonuclease P database

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Compilation of tRNA sequences and sequences of tRNA genes

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermodynamics of coaxially stacked helixes with GA and CC mismatches

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data

13 July 2018

1 reference

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A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

A comparative database of group I intron structures

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

RNA hairpin loop stability depends on closing base pair

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

A periodic table of symmetric tandem mismatches in RNA.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

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The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles

13 July 2018

1 reference

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Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid)

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Theory of oligonucleotide stabilization. I. The effect of single-strand stacking.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Stability of ribonucleic acid double-stranded helices

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Characterization of RNA hairpin loop stability

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Phylogenetic comparative analysis of RNA secondary structure

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Improved predictions of secondary structures for RNA

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides.

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops

13 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermodynamic stabilities of internal loops with GU closing pairs in RNA.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Fast evaluation of internal loops in RNA secondary structure prediction.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermal unfolding of a group I ribozyme: the low-temperature transition is primarily disruption of tertiary structure.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635246

Protein-independent Folding Pathway of the 16S rRNA 5′ Domain

27 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKL472

Predicting thermodynamic properties of RNA

21 January 2018

1 reference

12 December 2020

Improved parameters for the prediction of RNA hairpin stability

1 reference

12 December 2020

Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA

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12 December 2020

The Signal Recognition Particle Database (SRPDB)

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12 December 2020

Free energy of imperfect nucleic acid helices. I. The bulge defect

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12 December 2020

The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA

1 reference

12 December 2020

Thermodynamics of three-way multibranch loops in RNA

1 reference

12 December 2020

Stability of RNA hairpins closed by wobble base pairs

1 reference

12 December 2020

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

1 reference

12 December 2020

Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp

1 reference

12 December 2020

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing — a review

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

Major groove accessibility of RNA

1 reference

12 December 2020

A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides

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

Identifiers

DOI

10.1093/NAR/GKL472

1 reference

6 August 2017

1 reference

6 August 2017

1 reference