ArticleNucleic acids research2000
PseudoBase: a database with RNA pseudoknots.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- Directed evolution of small RNA-stabilizing motifs that improve prime-editing efficiency.Nature biotechnology · 2026Article
- Replication of alphaviruses requires a pseudoknot that involves the poly(A) tail.RNA (New York, N.Y.) · 2022Article
- Role of an RNA pseudoknot involving the polyA tail in replication of Pepino mosaic potexvirus and related plant viruses.Scientific reports · 2022Article
- RNA folding using quantum computers.PLoS computational biology · 2022Article
- Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution.Science advances · 2021Article
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- bpRNA: large-scale automated annotation and analysis of RNA secondary structure.Nucleic acids research · 2018Article
- Synthesizing topological structures containing RNA.Nature communications · 2017Article
- Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach.Journal of molecular biology · 2016Article
- An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.Frontiers in genetics · 2016Article
- A Dynamic 3D Graphical Representation for RNA Structure Analysis and Its Application in Non-Coding RNA Classification.PloS one · 2016Article
- Multi-objective optimization for RNA design with multiple target secondary structures.BMC bioinformatics · 2015Article
- Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores.BMC bioinformatics · 2015Article
- Characteristics and prediction of RNA structure.BioMed research international · 2014Article
- Tuning a riboswitch response through structural extension of a pseudoknot.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Efficient known ncRNA search including pseudoknots.BMC bioinformatics · 2013Article
- Predicting pseudoknotted structures across two RNA sequences.Bioinformatics (Oxford, England) · 2012Article
- Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.Nucleic acids research · 2012Article
- Multi-objective genetic algorithm for pseudoknotted RNA sequence design.Frontiers in genetics · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio. Leiden Univ.nl/ approximately Batenburg/PKB.html. This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.
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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.