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Protocols

RNAstructure specifications

Information


Unique identifier OMICS_03455
Name RNAstructure
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 5.8.1
Stability Stable
Registration required Yes
Maintained Yes

Subtools


  • AccessFold
  • AllSub
  • bifold
  • bipartition
  • CircleCompare
  • ct2dot
  • CycleFold, TurboKnot
  • dot2ct Draw
  • DuplexFold
  • Dynalign II
  • efn2
  • EnsembleEnergy
  • Fold
  • oligoscreen OligoWalk
  • partition
  • PARTS
  • ProbablePair
  • RemovePseudoknots
  • stochastic TurboFold

Download


conda.png

Versioning


No version available

Maintainer


  • person_outline David H. Mathews <>

Additional information


http://rna.urmc.rochester.edu/RNAstructureHelp.html http://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html

Information


Unique identifier OMICS_03455
Name RNAstructure
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable

Subtools


  • AccessFold
  • AllSub
  • bifold
  • bipartition
  • CircleCompare
  • ct2dot
  • CycleFold, TurboKnot
  • dot2ct Draw
  • DuplexFold
  • Dynalign II
  • efn2
  • EnsembleEnergy
  • Fold
  • oligoscreen OligoWalk
  • partition
  • PARTS
  • ProbablePair
  • RemovePseudoknots
  • stochastic TurboFold

Maintainer


This tool is not maintained anymore.

Additional information


http://rna.urmc.rochester.edu/RNAstructureHelp.html http://rna.urmc.rochester.edu/RNAstructureWeb/Information/Help.html

Publications for RNAstructure

RNAstructure citations

 (92)
library_books

Ribosome dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE

2018
PMCID: 5882922
PMID: 29615727
DOI: 10.1038/s41598-018-23845-x

[…] free energy of hybridization and the free energy required for making the interaction sites accessible., the rna secondary structure of the ires element under different conditions was predicted using rnastructure imposing shape reactivity values as pseudo-free energy change constraints together with nearest neighbor thermodynamic parameters using -0.8 kcal/mol and 2.6 for the intercept (b) […]

library_books

Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory

2018
PMCID: 5836418
PMID: 29506466
DOI: 10.1186/s12859-018-2078-5

[…] [, ]. however less focus has been given to the mutual information between the basepairs of a single rna molecule. using the nearest neighbor model (excluding pseudoknots), as implemented in the rnastructure package [], our algorithm finds the basepairs that provide the most information about other basepairs: the most informative base pairs (mibps). we then visualize the effect […]

library_books

Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes

2018
PMCID: 5807309
PMID: 29426922
DOI: 10.1038/s41467-018-02923-8

[…] comparable, with both sleq and ring-map deviating by a few percents from ground truth in estimating allele population fractions. to compare predicted structures, we fed ring-map’s output profiles to rnastructure—predicted structures were close to both the references and sleq’s predictions. the complete details are found in supplementary methods. it is worth noting, however, that by summarizing […]

library_books

Structural analyses of NEAT1 lncRNAs suggest long range RNA interactions that may contribute to paraspeckle architecture

2018
PMCID: 5909464
PMID: 29394378
DOI: 10.1093/nar/gky046

[…] to 0.35 by using in vitro transcribed and probed tetrahymena p4p6 domain () () as a positive control., rna secondary structure models with or without shape probing constraints were generated using rnastructure software (linux text interface 64 bit, version 5.8.1; default parameters) (). shape reactivity scores were used as constraints for rna secondary structure predictions. to generate rna […]

library_books

Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four dimensional chemical mapping

2018
PMCID: 5847336
PMID: 29446752
DOI: 10.7554/eLife.29602.097

[…] structures, potentially many at low frequencies, beyond those detected here in the ligand-free ensembles., in silico rna shape profiles were simulated using the partition executable from the rnastructure package version 5.6 (; ). the resulting pair-wise probability matrices was projected into a one-dimensional vector to get per-residue base pairing probabilities (bpp). for m2r quartet […]

library_books

Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias

2017
PMCID: 5772840
PMID: 29387823
DOI: 10.1016/j.heliyon.2017.e00492

[…] most g:u hydrogen bonds do not actually form for thermodynamic reasons; accordingly, the calculated δg of this hypothetical hairpin was only – 6 kcal by mfold, and attempts to fold this sequence in rnastructure returned the message “this structure contains no pairs”. in this particular example, even if the hairpin were to form in vivo, any ribosomal slowdown promoted by it would actually help […]


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RNAstructure institution(s)
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA; Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
RNAstructure funding source(s)
Supported by National Institutes of Health (NIH) [R01 GM076485].

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