ArticleNucleic acids research2009
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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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.
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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.
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Who cites it
29 citing papers in PubMed.
- Exploring the Boundaries of Modern Quantum Annealers with RNA Structure Prediction.The journal of physical chemistry. B · 2026Article
- Ribonanza: deep learning of RNA structure through dual crowdsourcing.bioRxiv : the preprint server for biology · 2024Article
- Knotify_V2.0: Deciphering RNA Secondary Structures with H-Type Pseudoknots and Hairpin Loops.Genes · 2024Article
- Possible involvement of three-stemmed pseudoknots in regulating translational initiation in human mRNAs.PloS one · 2024Article
- Knotify+: Toward the Prediction of RNA H-Type Pseudoknots, Including Bulges and Internal Loops.Biomolecules · 2023Article
- Metrics for RNA Secondary Structure Comparison.Methods in molecular biology (Clifton, N.J.) · 2023Article
- aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.BMC bioinformatics · 2022Article
- RNA folding using quantum computers.PLoS computational biology · 2022Article
- Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.Science advances · 2021Article
- High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove.Nature structural & molecular biology · 2019Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- An algebraic language for RNA pseudoknots comparison.BMC bioinformatics · 2019Article
- Bi-objective integer programming for RNA secondary structure prediction with pseudoknots.BMC bioinformatics · 2018Article
- RNA inverse folding using Monte Carlo tree search.BMC bioinformatics · 2017Article
- Pseudoknots in RNA folding landscapes.Bioinformatics (Oxford, England) · 2016Article
- URS DataBase: universe of RNA structures and their motifs.Database : the journal of biological databases and curation · 2016Article
- DSSR: an integrated software tool for dissecting the spatial structure of RNA.Nucleic acids research · 2015Article
- antaRNA--Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization.BMC bioinformatics · 2015Article
- Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.BMC bioinformatics · 2015Article
- Structural determinants for ligand capture by a class II preQ1 riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Pseudoknots have been recognized to be an important type of RNA secondary structures responsible for many biological functions. PseudoBase, a widely used database of pseudoknot secondary structures developed at Leiden University, contains over 250 records of pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments and sequence comparisons. To promptly address the growing analysis requests of the researchers on RNA structures and bring together information from multiple sources across the Internet to a single platform, we designed and implemented PseudoBase++, an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ (http://pseudobaseplusplus.utep.edu) maps the PseudoBase dataset into a searchable relational database including additional functionalities such as pseudoknot type. PseudoBase++ links each pseudoknot in PseudoBase to the GenBank record of the corresponding nucleotide sequence and allows scientists to automatically visualize RNA secondary structures with PseudoViewer. It also includes the capabilities of fine-grained reference searching and collecting new pseudoknot information.
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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.