ArticlePeerJ2022
ScanFold 2.0: a rapid approach for identifying potential structured RNA targets in genomes and transcriptomes.
Article in PeerJ, 2022. 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, 23 citations in OpenAlex.
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- RNAStructuromeDB: a transcriptome-wide database of predicted RNA secondary structures with integrated APIs for functional annotation and RNA-targeted drug discovery.NAR genomics and bioinformatics · 2026Article
- Discontinuous EBOV RNA synthesis events in patients with Ebola virus disease and their relationship to viral load and outcome of infection.Journal of virology · 2025Article
- Identification of conserved RNA secondary structures in human respiratory syncytial virus A (hRSV A).NAR genomics and bioinformatics · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Transcriptome-wide prediction of heat-sensitive RNA structures inFrontiers in plant science · 2025Article
- Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40.British journal of pharmacology · 2024Review
- Transcriptome-Wide, Unbiased Profiling of Ribonuclease Targeting Chimeras.Journal of the American Chemical Society · 2024Article
- Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop.Biochemistry · 2024Article
- Heterobifunctional small molecules to modulate RNA function.Trends in pharmacological sciences · 2024Review
- Speciation, natural selection, and networks: three historians versus theoretical population geneticists.Theory in biosciences = Theorie in den Biowissenschaften · 2024Review
- Article
- Discovery of RNA secondary structural motifs using sequence-ordered thermodynamic stability and comparative sequence analysis.MethodsX · 2023Article
- Broad-spectrum metastasis suppressing compounds and therapeutic uses thereof in human tumors.Scientific reports · 2023Article
- Advances in treatment strategies for COVID-19: Insights from other coronavirus diseases and prospects.Biosafety and health · 2023Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
A major limiting factor in target discovery for both basic research and therapeutic intervention is the identification of structural and/or functional RNA elements in genomes and transcriptomes. This was the impetus for the original ScanFold algorithm, which provides maps of local RNA structural stability, evidence of sequence-ordered (potentially evolved) structure, and unique model structures comprised of recurring base pairs with the greatest structural bias. A key step in quantifying this propensity for ordered structure is the prediction of secondary structural stability for randomized sequences which, in the original implementation of ScanFold, is explicitly evaluated. This slow process has limited the rapid identification of ordered structures in large genomes/transcriptomes, which we seek to overcome in this current work introducing ScanFold 2.0. In this revised version of ScanFold, we no longer explicitly evaluate randomized sequence folding energy, but rather estimate it using a machine learning approach. For high randomization numbers, this can increase prediction speeds over 100-fold compared to ScanFold 1.0, allowing for the analysis of large sequences, as well as the use of additional folding algorithms that may be computationally expensive. In the testing of ScanFold 2.0, we re-evaluate the Zika, HIV, and SARS-CoV-2 genomes and compare both the consistency of results and the time of each run to ScanFold 1.0. We also re-evaluate the SARS-CoV-2 genome to assess the quality of ScanFold 2.0 predictions
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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.