ArticleNucleic acids research2016
incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- 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
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.BMC bioinformatics · 2022Article
- 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
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- Machine Learning to Enhance Biophysical Models for Riboswitch Discovery.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv.
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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.