ArticleNature methods2011
Sequence-based identification of 3D structural modules in RNA with RMDetect.
Article in Nature methods, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed, 94 citations in OpenAlex.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- All-at-once RNA folding with 3D motif prediction framed by evolutionary information.Nature methods · 2025Article
- Review
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- Classification and Identification of Non-canonical Base Pairs and Structural Motifs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.Bioinformatics (Oxford, England) · 2023Article
- Review
- Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells.Nature communications · 2022Article
- Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.Nucleic acids research · 2021Article
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- Augmented base pairing networks encode RNA-small molecule binding preferences.Nucleic acids research · 2020Article
- RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools.Nucleic acids research · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.Nucleic acids research · 2019Article
- Using Rosetta for RNA homology modeling.Methods in enzymology · 2019Article
- Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.Nucleic acids research · 2018Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structural RNA modules, sets of ordered non-Watson-Crick base pairs embedded between Watson-Crick pairs, have central roles as architectural organizers and sites of ligand binding in RNA molecules, and are recurrently observed in RNA families throughout the phylogeny. Here we describe a computational tool, RNA three-dimensional (3D) modules detection, or RMDetect, for identifying known 3D structural modules in single and multiple RNA sequences in the absence of any other information. Currently, four modules can be searched for: G-bulge loop, kink-turn, C-loop and tandem-GA loop. In control test sequences we found all of the known modules with a false discovery rate of 0.23. Scanning through 1,444 publicly available alignments, we identified 21 yet unreported modules and 141 known modules. RMDetect can be used to refine RNA 2D structure, assemble RNA 3D models, and search and annotate structured RNAs in genomic data.
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