ArticleNucleic acids research2005
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers, 1 of them a synthesis that pooled it.
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
119 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Engineering polymeric RNA scaffolds as programmable combinatorial innate immune agonists.Nucleic acids research · 2026Article
- Expression of nano-engineered RNA organelles in bacteria.Nature communications · 2026Article
- 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
- Targeting Glioblastoma Stem Cells via EphA2: Structural Insights into the RNA Aptamer A40s for Precision Therapy.Journal of chemical information and modeling · 2025Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Co-transcriptional production of programmable RNA condensates and synthetic organelles.Nature nanotechnology · 2024Article
- N6-methyladenosine modification of a parvovirus-encoded small noncoding RNA facilitates viral DNA replication through recruiting Y-family DNA polymerases.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs.PloS one · 2024Article
- A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- DrForna: visualization of cotranscriptional folding.Bioinformatics (Oxford, England) · 2023Article
- Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi.Nature communications · 2023Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogenbioRxiv : the preprint server for biology · 2023Article
- DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.Bioinformatics (Oxford, England) · 2023Article
- Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application.Biosensors · 2022Review
59 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically 'entangled' helices (i.e. knots) are efficiently predicted taking into account simple geometrical and topological constraints. To encourage interactivity, simulations launched as immediate jobs are automatically stopped after a few seconds and return adapted recommendations. Users can then choose to continue incomplete simulations using the batch queuing system or go back and modify suggested options in their initial query. Detailed output provide (i) a series of low free energy structures, (ii) an online animated folding path and (iii) a programmable trajectory plot focusing on a few helices of interest to each user. The service can be accessed at http://kinefold.curie.fr/.
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.