ArticleRNA (New York, N.Y.)2010
ProbKnot: fast prediction of RNA secondary structure including pseudoknots.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
114 citing papers in PubMed.
- VARIANT: Web Server for Decoding and Analyzing Viral Mutations at Genome and Protein Levels.Biophysical journal · 2026Article
- Hierarchical breakdown of RNA structure prediction in CASP16: from reliable local helices to speculative multimer assembly.Bioinformatics (Oxford, England) · 2026Article
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Machine learning for RNA secondary structure prediction: a review of current methods and challenges.RNA (New York, N.Y.) · 2026Review
- Kinetic Traps in RNA Folding: Targeted Design of Frameshifting Element Mutants by Thermodynamic and Kinetic Analysis of the Chikungunya Virus.The journal of physical chemistry. B · 2026Article
- A ribosome-bound pseudoknot in the HCV coding region stimulates viral growth by tuning viral translation.Cell reports · 2026Article
- NTFold: Structure-Sensing Nucleotide Attention Learning for RNA Secondary Structure Prediction.Sensors (Basel, Switzerland) · 2026Article
- Innovative design and comprehensive characterization of a valine-enhanced lipid nanoparticle-coated mRNA vaccine targeting the SARS-CoV-2 S-RBD antigen.Scientific reports · 2025Article
- AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.bioRxiv : the preprint server for biology · 2025Article
- Enhanced RNA secondary structure prediction through integrative deep learning and structural context analysis.Nucleic acids research · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- RNA secondary structure prediction by conducting multi-class classifications.Computational and structural biotechnology journal · 2025Article
- A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.PloS one · 2025Article
- Identification and characterization of mycoviruses in transcriptomes from the fungal family ceratocystidaceae.Virus genes · 2024Article
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- Knotify_V2.0: Deciphering RNA Secondary Structures with H-Type Pseudoknots and Hairpin Loops.Genes · 2024Article
- sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.Briefings in bioinformatics · 2024Article
- DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning.Journal of chemical information and modeling · 2024Article
- Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials.Communications biology · 2024Article
- Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs.PloS one · 2024Article
54 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
It is a significant challenge to predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots of any topology, ProbKnot, is reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities in O(N(2)) time, where N is the length of the sequence. The performance of ProbKnot was measured by comparing predicted structures with known structures for a large database of RNA sequences with fewer than 700 nucleotides. The percentage of known pairs correctly predicted was 69.3%. Additionally, the percentage of predicted pairs in the known structure was 61.3%. This performance is the highest of four tested algorithms that are capable of pseudoknot prediction. The program is available for download at: http://rna.urmc.rochester.edu/RNAstructure.html.
Indexed as
Identifiers
What OpenQuestion holds
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.