ArticleRNA (New York, N.Y.)2008
Analysis and classification of RNA tertiary structures.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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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
33 citing papers in PubMed.
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Structural Landscape of nsp Coding Genomic Regions of SARS-CoV-2-ssRNA Genome: A Structural Genomics Approach Toward Identification of Druggable Genome, Ligand-Binding Pockets, and Structure-Based Druggability.Molecular biotechnology · 2024Article
- RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.NAR genomics and bioinformatics · 2023Article
- Underestimated Aspects in Male Infertility: Epigenetics is A New Approach in Men with Obesity or Diabetes: A Review.International journal of fertility & sterility · 2022Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- Responsive self-assembly of tectoRNAs with loop-receptor interactions from the tetrahydrofolate (THF) riboswitch.Nucleic acids research · 2019Article
- The genome sequence of 'Kurodagosun', a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding.Molecular genetics and genomics : MGG · 2018Article
- Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy.Cancer letters · 2018Review
- Advancement of the Emerging Field of RNA Nanotechnology.ACS nano · 2017Review
- Article
- RAG-3D: a search tool for RNA 3D substructures.Nucleic acids research · 2015Article
- RASS: a web server for RNA alignment in the joint sequence-structure space.Nucleic acids research · 2014Article
- SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments.Nucleic acids research · 2014Article
- RNA Bricks--a database of RNA 3D motifs and their interactions.Nucleic acids research · 2014Article
- RNA nanotechnology for computer design and in vivo computation.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2013Article
- Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells.Nature protocols · 2013Article
- SETTER: web server for RNA structure comparison.Nucleic acids research · 2012Article
- Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity.Nucleic acids research · 2012Article
- Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
There is a fast growing interest in noncoding RNA transcripts. These transcripts are not translated into proteins, but play essential roles in many cellular and pathological processes. Recent efforts toward comprehension of their function has led to a substantial increase in both the number and the size of solved RNA structures. With the aim of addressing questions relating to RNA structural diversity, we examined RNA conservation at three structural levels: primary, secondary, and tertiary structure. Additionally, we developed an automated method for classifying RNA structures based on spatial (three-dimensional [3D]) similarity. Applying the method to all solved RNA structures resulted in a classified database of RNA tertiary structures (DARTS). DARTS embodies 1333 solved RNA structures classified into 94 clusters. The classification is hierarchical, reflecting the structural relationship between and within clusters. We also developed an application for searching DARTS with a new structure. The search is fast and its performance was successfully tested on all solved RNA structures since the creation of DARTS. A user-friendly interface for both the database and the search application is available online. We show intracluster and intercluster similarities in DARTS and demonstrate the usefulness of the search application. The analysis reveals the current structural repertoire of RNA and exposes common global folds and local tertiary motifs. Further study of these conserved substructures may suggest possible RNA domains and building blocks. This should be beneficial for structure prediction and for gaining insights into structure-function relationships.
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Registered trials
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