ArticleMethods in molecular biology (Clifton, N.J.)2025
Toward Increasing the Credibility of RNA Design.
Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Study on the Modification and Minding Mechanism of Bongkrekic Acid Aptamers for Food Safety.Foods (Basel, Switzerland) · 2026Article
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Factorization machine with quadratic-optimization annealing for RNA inverse folding and evaluation of binary-integer encoding and nucleotide assignment.Scientific reports · 2026Article
- Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks.Non-coding RNA · 2025Article
- R3Design: deep tertiary structure-based RNA sequence design and beyond.Briefings in bioinformatics · 2024Article
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Authors and funding
2 authors.
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Abstract
In the problem of RNA design, also known as inverse folding, RNA sequences are predicted that achieve the desired secondary structure at the lowest possible free energy and under certain constraints. The designed sequences have applications in synthetic biology and RNA-based nanotechnologies. There are also known cases of the successful use of inverse folding to discover previously unknown noncoding RNAs. Several computational methods have been dedicated to the problem of RNA design. They differ by algorithm and additional parameters, e.g., those determining the goal function in the sequence optimization process. Users can obtain many promising RNA sequences quite easily. The more difficult issue is to critically evaluate them and select the most favorable and reliable sequence that form1s the expected RNA structure. The latter problem is addressed in this paper. We propose an RNA design protocol extended to include sequence evaluation, for which a 3D structure is used. Experiments show that the accuracy of RNA design can be improved by adding a 3D structure prediction and analysis step.
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Registered trials
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