ArticleQuarterly reviews of biophysics2011
A new way to see RNA.
Article in Quarterly reviews of biophysics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- The RNA promoter for pathogenic orthoflaviviruses replication is universal and serves as target for viral inhibition.PLoS pathogens · 2026Article
- On the Completeness of Existing RNA Fragment Structures.Genomics, proteomics & bioinformatics · 2025Article
- Prevalence of dual-donating amines in key regions of functional RNAs.RNA (New York, N.Y.) · 2025Article
- Article
- Systematic analysis of biomolecular conformational ensembles with PENSA.The Journal of chemical physics · 2025Article
- lociPARSE: A Locality-aware Invariant Point Attention Model for Scoring RNA 3D Structures.Journal of chemical information and modeling · 2024Article
- RNAtango: Analysing and comparing RNA 3D structures via torsional angles.PLoS computational biology · 2024Article
- Origins of Life: The Protein Folding Problem all over again?Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- lociPARSE: a locality-aware invariant point attention model for scoring RNA 3D structures.bioRxiv : the preprint server for biology · 2024Article
- The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids.Nucleic acids research · 2024Article
- The pseudotorsional space of RNA.RNA (New York, N.Y.) · 2023Article
- RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures.Bioinformatics (Oxford, England) · 2021Article
- Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family.Nature chemical biology · 2020Article
- Understanding the binding specificities of mRNA targets by the mammalian Quaking protein.Nucleic acids research · 2019Article
- Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures.Nucleic acids research · 2019Article
- Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling.Nature communications · 2017Article
- Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein.Scientific reports · 2017Article
- Crystal structure of group II intron domain 1 reveals a template for RNA assembly.Nature chemical biology · 2015Article
- ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid.Journal of the American Society for Mass Spectrometry · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.
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What OpenQuestion holds
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.