ArticleNucleic acids research2015
RAG-3D: a search tool for RNA 3D substructures.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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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Who cites it
27 citing papers in PubMed.
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.Biology · 2026Article
- How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.PLoS computational biology · 2025Article
- A Cascade of Conformational Switches in SARS-CoV-2 Frameshifting: Coregulation by Upstream and Downstream Elements.Biochemistry · 2025Article
- RNA fold prediction by Monte Carlo in graph space and the statistical mechanics of tertiary interactions.RNA (New York, N.Y.) · 2024Article
- An intricate balancing act: Upstream and downstream frameshift co-regulatory elements.bioRxiv : the preprint server for biology · 2024Article
- RNAloops: a database of RNA multiloops.Bioinformatics (Oxford, England) · 2022Article
- RNA-As-Graphs Motif Atlas-Dual Graph Library of RNA Modules and Viral Frameshifting-Element Applications.International journal of molecular sciences · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Nature communications · 2022Article
- Length-dependent motions of SARS-CoV-2 frameshifting RNA pseudoknot and alternative conformations suggest avenues for frameshifting suppression.Research square · 2022Article
- Structure-altering mutations of the SARS-CoV-2 frameshifting RNA element.Biophysical journal · 2021Article
- A Fiedler Vector Scoring Approach for Novel RNA Motif Selection.The journal of physical chemistry. B · 2021Article
- Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element.bioRxiv : the preprint server for biology · 2020Article
- Identification of novel RNA design candidates by clustering the extended RNA-As-Graphs library.Biochimica et biophysica acta. General subjects · 2020Article
- Inverse folding with RNA-As-Graphs produces a large pool of candidate sequences with target topologies.Journal of structural biology · 2020Article
- RAG-Web: RNA structure prediction/design using RNA-As-Graphs.Bioinformatics (Oxford, England) · 2020Article
- NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes.Nucleic acids research · 2019Article
- An extended dual graph library and partitioning algorithm applicable to pseudoknotted RNA structures.Methods (San Diego, Calif.) · 2019Article
- A pipeline for computational design of novel RNA-like topologies.Nucleic acids research · 2018Article
- Dual Graph Partitioning Highlights a Small Group of Pseudoknot-Containing RNA Submotifs.Genes · 2018Article
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Authors and funding
4 authors.
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Abstract
To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.
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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.