ArticleBioinformatics (Oxford, England)2015
The RNA shapes studio.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Genetic mechanisms underlying the structural elaboration and dissemination of viral internal ribosomal entry sites.Nucleic acids research · 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
- Decoding RNA triple helices: identification from sequence and secondary structure.Briefings in bioinformatics · 2026Article
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- Targeting Glioblastoma Stem Cells via EphA2: Structural Insights into the RNA Aptamer A40s for Precision Therapy.Journal of chemical information and modeling · 2025Article
- Ex.50.T aptamer impairs tumor-stroma cross-talk in breast cancer by targeting gremlin-1.Cell death discovery · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
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- A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.PloS one · 2025Article
- Simulated Annealing for RNA Design with SIMARD.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evaluating Performance of Different RNA Secondary Structure Prediction Programs Using Self-cleaving Ribozymes.Genomics, proteomics & bioinformatics · 2024Article
- Nucleocapsids of the Rift Valley fever virus ambisense S segment contain an exposed RNA element in the center that overlaps with the intergenic region.Nature communications · 2024Article
- Universal cold RNA phase transitions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Xinyang flavivirus, fromThe Journal of general virology · 2024Article
- Widespread Horizontal Gene Transfer Among Animal Viruses.bioRxiv : the preprint server for biology · 2024Article
- Accurate prediction of RNA secondary structure including pseudoknots through solving minimum-cost flow with learned potentials.Communications biology · 2024Article
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- Classified Dynamic Programming in RNA Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
19 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
No grant is acknowledged in the PubMed record.
Abstract
motivationAbstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.
resultsWe have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNAshapes, RNAalishapes and pknotsRG, including its recent extension pKiss. As a spin-off, we obtain heretofore unavailable functionality: e. g. with pKiss, we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool pAliKiss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways. AVAILABILITY AND IMPLEMENTATION: As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio. CONTACT: bibi-help@cebitec.uni-bielefeld.de.
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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.