ArticleNucleic acids research2021
MoiRNAiFold: a novel tool for complex in silico RNA design.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- RNAtranslator: Modeling protein-conditional RNA design as sequence-to-sequence natural language translation.PLoS computational biology · 2025Article
- Computational De Novo Design of Group II Introns Yields Highly Active Ribozymes.Chembiochem : a European journal of chemical biology · 2025Article
- Comprehensive datasets for RNA design, machine learning, and beyond.Scientific reports · 2025Article
- DRAG: design RNAs as hierarchical graphs with reinforcement learning.Briefings in bioinformatics · 2025Article
- DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.Nucleic acids research · 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
- Complex In Silico RNA Design with MoiRNAiFold.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Datasets for Benchmarking RNA Design Algorithms.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.Interdisciplinary sciences, computational life sciences · 2022Article
- aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.BMC bioinformatics · 2022Article
- End-to-end computational approach to the design of RNA biosensors for detecting miRNA biomarkers of cervical cancer.Synthetic and systems biotechnology · 2022Article
- Correction to 'MoiRNAiFold: a novel tool for complex in silico RNA design'.Nucleic acids research · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).
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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.