ArticleNucleic acids research2016
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 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
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- Identification of 3D motifs in Rfam with JAR3D.RNA (New York, N.Y.) · 2026Article
- Article
- New targets and procedures for validating the valence geometry of nucleic acid structures.Nucleic acids research · 2026Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- RNA three-dimensional structure drives the sequence organization of potato spindle tuber viroid quasispecies.PLoS pathogens · 2024Article
- Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework.Bioinformatics (Oxford, England) · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Protein-RNA interaction prediction with deep learning: structure matters.Briefings in bioinformatics · 2022Article
- Augmented base pairing networks encode RNA-small molecule binding preferences.Nucleic acids research · 2020Article
- A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana.PLoS pathogens · 2019Article
- Article
- Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function.Circulation research · 2018Review
- Opportunities and Challenges in RNA Structural Modeling and Design.Biophysical journal · 2017Article
- Bioinformatic tools for analysis of CLIP ribonucleoprotein data.Wiley interdisciplinary reviews. RNA · 2017Review
- Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.Nucleic acids research · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
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5 authors.
Funding
Abstract
Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson-Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time.
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