ReviewMethods (San Diego, Calif.)2016
The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.
Review in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage.Chemical science · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species.Bioinformatics (Oxford, England) · 2024Article
- Machine-learned molecular mechanics force fields from large-scale quantum chemical data.Chemical science · 2024Article
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.Nucleic acids research · 2024Article
- Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- Lone Pair…π Contacts and Structure Signatures of r(UNCG) Tetraloops, Z-Turns, and Z-Steps: A WebFR3D Survey.Molecules (Basel, Switzerland) · 2022Article
- RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures.Frontiers in bioinformatics · 2021Article
- Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles.Nature protocols · 2020Article
- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- RNA CoSSMos 2.0: an improved searchable database of secondary structure motifs in RNA three-dimensional structures.Database : the journal of biological databases and curation · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation.Nucleic acids research · 2019Article
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
- Article
- Fluorogenic RNA Aptamers: A Nano-platform for Fabrication of Simple and Combinatorial Logic Gates.Nanomaterials (Basel, Switzerland) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs.
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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.