ArticleBMC bioinformatics2015
antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Control of gene output by intron RNA structure.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive datasets for RNA design, machine learning, and beyond.Scientific reports · 2025Article
- Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks.Non-coding RNA · 2025Article
- RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models.Bioinformatics (Oxford, England) · 2024Article
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- Computational design and experimental verification of pseudoknotted ribozymes.RNA (New York, N.Y.) · 2023Article
- Self-evoluting framework of deep convolutional neural network for multilocus protein subcellular localization.Medical & biological engineering & computing · 2020Article
- High-throughput interrogation of programmed ribosomal frameshifting in human cells.Nature communications · 2020Article
- EternaBrain: Automated RNA design through move sets and strategies from an Internet-scale RNA videogame.PLoS computational biology · 2019Article
- Fixed-parameter tractable sampling for RNA design with multiple target structures.BMC bioinformatics · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- RNA inverse folding using Monte Carlo tree search.BMC bioinformatics · 2017Article
- An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.Frontiers in genetics · 2016Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA's 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures into the design. Hairpin-(H)- and kissing hairpin-(K)-type pseudoknots cover a wide range of biologically functional pseudoknots and can be represented on a secondary structure level.
resultsThe RNA inverse folding program antaRNA, which takes secondary structure, target GC-content and sequence constraints as input, is extended to provide solutions for such H- and K-type pseudoknotted secondary structure constraint. We demonstrate the easy and flexible interchangeability of modules within the antaRNA framework by incorporating pKiss as structure prediction tool capable of predicting the mentioned pseudoknot types. The performance of the approach is demonstrated on a subset of the Pseudobase ++ dataset.
conclusionsThis new service is available via a standalone version and is also part of the Freiburg RNA Tools webservice. Furthermore, antaRNA is available in Galaxy and is part of the RNA-workbench Docker image.
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