ArticleNucleic acids research2015
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs.Algorithms for molecular biology : AMB · 2025Article
- A NovelBiomolecules · 2025Article
- RNA Design Using incaRNAfbinv Demonstrated with the Identification of Functional RNA Motifs in Hepatitis Delta Virus.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- Theoretical basis for stabilizing messenger RNA through secondary structure design.Nucleic acids research · 2021Article
- MoiRNAiFold: a novel tool for complex in silico RNA design.Nucleic acids research · 2021Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data.PLoS computational biology · 2018Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- RNAblueprint: flexible multiple target nucleic acid sequence design.Bioinformatics (Oxford, England) · 2017Article
- New tools to analyze overlapping coding regions.BMC bioinformatics · 2016Article
- RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.BMC bioinformatics · 2016Article
- incaRNAfbinv: a web server for the fragment-based design of RNA sequences.Nucleic acids research · 2016Article
- RNAiFold2T: Constraint Programming design of thermo-IRES switches.Bioinformatics (Oxford, England) · 2016Article
- Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.Scientific reports · 2016Article
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3 authors.
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Abstract
unlabelledSeveral algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. AVAILABILITY: the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0.
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