ArticleNucleic acids research2021
TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.RNA (New York, N.Y.) · 2024Article
- An ontology-based knowledge graph for representing interactions involving RNA molecules.Scientific data · 2024Article
- Translational T-box riboswitches bind tRNA by modulating conformational flexibility.Nature communications · 2024Article
- Recognition of the tRNA structure: Everything everywhere but not all at once.Cell chemical biology · 2024Review
- Ribocentre-switch: a database of riboswitches.Nucleic acids research · 2024Article
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- Streptococcus suis TrpX is part of a tryptophan uptake system, and its expression is regulated by a T-box regulatory element.Scientific reports · 2022Article
- Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action.Nucleic acids research · 2022Article
- Cooperativity and Interdependency between RNA Structure and RNA-RNA Interactions.Non-coding RNA · 2021Review
- The Serine Biosynthesis ofInternational journal of molecular sciences · 2021Article
- The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.Nucleic acids research · 2021Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.
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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.