ViennaRNA Package 2.0
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BACKGROUND: Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties. RESULTS: The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions. CONCLUSIONS: The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
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The necessary level of wobbling may be provided by thermodynamics of RNA folding, as demonstrated in latest MCRS versions with actual nucleotide sequences and secondary structures calculated by ViennaRNA.
“The necessary level of wobbling may indeed be provided by the thermodynamics of RNA folding, as it has been demonstrated in the latest versions of MCRS [38], in which the purely phenotypic, sequence-implicit approach has been relaxed with the assignment of actual nucleotide sequences and the corresponding secondary structures (the latter calculated by the ViennaRNA algorithm [119] on the basis of”
From Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems (2017) · cites this paper as [119]
ψ and m1ψ substitutions for U have been widely adopted for mRNA therapeutics and vaccines due to improved in-cell translation and better control of innate immune responses.
“In particular, we focused on ψ and m1ψ, since these substitutions for U have been widely adopted for mRNA therapeutics and vaccines due to improved in-cell translation and to better control of innate immune responses2,3,8,67 through avoidance of recognition by cellular toll-like receptors (TLR7 and TLR8)68, RIG‑I, and PKR69–71.”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [67]
The Background section discusses computational RNA folding and RNA–RNA interactions, not the use of ψ or m1ψ in mRNA therapeutics or vaccines. Searches for those substitutions, in-cell translation, and innate immune receptors found no passage addressing the attributed claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredThe effect of base composition on folding energy can be deduced from nearest-neighbor models of RNA folding.
“The effect of base composition on folding energy can be deduced from nearest-neighbor models of RNA folding (Kennedy et al. 2010; Lorenz et al. 2011; Derr et al. 2012)”
From The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability (2013) · cites this paper as Lorenz et al. 2011
ψ and derivatives have been reported to stabilize mRNAs against decay in cells.
“While ψ and derivatives have been reported to stabilize mRNAs against decay in cells67, the effects of these modifications on mRNA stability in solution have not been reported.”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [67]
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“Widely used systems such as RNAstructure (Mathews and Turner, 2006), Vienna RNAfold (Lorenz etal.”
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BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
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ESRP2–microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation
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- Authors
- Lorenz, R., Bernhart, S. H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P. F., & Hofacker, I. L.
- Affiliations
- University of Vienna (AT)
- Leipzig University (DE)
- University of Copenhagen (DK)
- Corresponding author
- Lorenz, Ronny
- Hofacker, Ivo L
- Venue
- Algorithms for Molecular Biology
- Published
- 2011-11-24
- Volume
- 6
- Issue
- 1
- Pages
- 26-26
- ISSN
- 1748-7188 (ISSN-L)
- PMC
- PMC3319429
- OpenAlex
- W2086561953
- Cited by
- 5,098
- References
- 108
- Citations by year
- 2026: 546 · 2025: 574 · 2024: 555 · 2023: 441 · 2022: 448 · 2021: 494 · 2020: 444 · 2019: 341 · 2018: 298 · 2017: 287 · 2016: 242 · 2015: 197 · 2014: 124 · 2013: 77 · 2012: 27
- FWCI
- 29.58
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Algorithms for Molecular Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Phaidra (Universität Wien) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Fraunhofer-Publica (Fraunhofer-Gesellschaft) (submittedVersion)
- Funders
- European Commission
- Deutsche Forschungsgemeinschaft (STA 850/7-1)
- Austrian Science Fund (SFB F43, SFB F43 RNA)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- RNA secondary structure, RNA folding, thermodynamic parameters, base pairing probability, RNA-RNA interactions, Z-score, OpenMP parallel computing, nucleic acid folding
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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