ArticleAlgorithms for molecular biology : AMB2011
ViennaRNA Package 2.0.
Article in Algorithms for molecular biology : AMB, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3,174 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3,174 citing papers in PubMed.
- N-terminal fusion length: The key to reliable and context-preserving regulatory sequence characterization.Synthetic and systems biotechnology · 2027Article
- Inducible Protein Knockdown via Engineered Small RNAs in Chlamydia.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Visualization of RNA Structures and Functional Annotations Using ArcPlot.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Functional analysis ofMolecular therapy. Nucleic acids · 2026Article
- AptViralDB: A repository of experimentally validated antiviral aptamers.Molecular therapy. Nucleic acids · 2026Review
- Discovery of a mutation-containing circRNA in polyglutamine disease through systematic analysis of RNAs with CAG repeats.RNA biology · 2026Article
- Impact of interspecies colostrum and milk replacement on circulating sncRNA dynamics of neonatal goat kids.RNA biology · 2026Article
- In silico unwinding ofRNA biology · 2026Article
- A common germline 3' UTR variant controls DDIT4 translation efficiency and stress responses in cancer cells.iScience · 2026Article
- NanostarDB: an interactive knowledgebase for standardized annotation, discovery and reuse of nucleic acid nanostructure designs.Nature nanotechnology · 2026Article
- Effects of RyhB on Fur regulation of cytochromeApplied and environmental microbiology · 2026Article
- Genome-wide characterization of DUB genes in Betula platyphylla and BpUBP3 function in pollen tube growth.Plant molecular biology · 2026Article
- Engineered human Argonaute 2 for targeted C-to-U RNA base editing.Nature biotechnology · 2026Article
- Methyltransferase RsmB chaperonesScience advances · 2026Article
- Article
- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- PUS7 mRNA pseudouridylation is driven by RNA sequence, structure, and cell-type-specific features.Cell genomics · 2026Article
- Design and in silico evaluation of PV-GNProtecta: an mRNA multi-epitope vaccine candidate against Puumala virus using immunoinformatics and structural analysis.Genomics & informatics · 2026Article
- Real-time single-molecule imaging in zebrafish embryos uncovers noncanonical translation.Science advances · 2026Article
3,114 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSecondary 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.
resultsThe 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.
conclusionsThe ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.