ArticleRNA (New York, N.Y.)2013
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- A large-scale cryo-EM RNA motif dataset and benchmark for machine learning-based structure modeling.Computational biology and chemistry · 2026Article
- Programmable Edge-to-Edge Assembly of RNA Nanostructures.ACS nano · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- A Large-Scale Cryo-EM RNA Motif Dataset and Benchmark for Machine Learning-Based Structure Modeling.bioRxiv : the preprint server for biology · 2026Article
- Exploring GNRA tetraloop-like motifs in nucleic acid 3D structures.Scientific reports · 2025Article
- All-at-once RNA folding with 3D motif prediction framed by evolutionary information.Nature methods · 2025Article
- Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input.bioRxiv : the preprint server for biology · 2025Article
- Improving RNA Secondary Structure Prediction Through Expanded Training Data.bioRxiv : the preprint server for biology · 2025Article
- GINClus: RNA structural motif clustering using graph isomorphism network.NAR genomics and bioinformatics · 2025Article
- Semi-supervised segmentation of RNA 3D structures using density-based clustering.Computational and structural biotechnology journal · 2025Article
- 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
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
- RNA3DB: A structurally-dissimilar dataset split for training and benchmarking deep learning models for RNA structure prediction.Journal of molecular biology · 2024Article
- FURNA: A database for functional annotations of RNA structures.PLoS biology · 2024Article
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- PERFUMES: pipeline to extract RNA functional motifs and exposed structures.Bioinformatics (Oxford, England) · 2024Article
- Classification and Identification of Non-canonical Base Pairs and Structural Motifs.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A systematic benchmark of machine learning methods for protein-RNA interaction prediction.Briefings in bioinformatics · 2023Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
44 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson-Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.
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