ArticleNucleic acids research2023
RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Crosstalk between RNA secondary and three-dimensional structure prediction: a comprehensive study.RNA biology · 2026Article
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- Computational approaches for RNA structure prediction and design.Cell reports. Physical science · 2026Article
- gCoSRNA: Generalizable Coaxial Stacking Prediction for RNA Junctions Using Secondary Structure.Biomolecules · 2026Article
- Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Enhancing RNA 3D Structure Prediction in CASP16: Integrating Physics-Based Modeling With Machine Learning for Improved Predictions.Proteins · 2026Article
- The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.Proteins · 2026Article
- Driving forces of RNA condensation revealed through coarse-grained modeling with explicit MgProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Generative AI for computational chemistry: A roadmap to predicting emergent phenomena.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- RNAbpFlow: Base pair-augmented SE(3)-flow matching for conditional RNA 3D structure generation.bioRxiv : the preprint server for biology · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- DeepRNA-Twist: language-model-guided RNA torsion angle prediction with attention-inception network.Briefings in bioinformatics · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Has AlphaFold3 achieved success for RNA?Acta crystallographica. Section D, Structural biology · 2025Article
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction.Bioinformatics (Oxford, England) · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
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2 authors.
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Abstract
RNA 3D structures are critical for understanding their functions. However, only a limited number of RNA structures have been experimentally solved, so computational prediction methods are highly desirable. Nevertheless, accurate prediction of RNA 3D structures, especially those containing multiway junctions, remains a significant challenge, mainly due to the complicated non-canonical base pairing and stacking interactions in the junction loops and the possible long-range interactions between loop structures. Here we present RNAJP ('RNA Junction Prediction'), a nucleotide- and helix-level coarse-grained model for the prediction of RNA 3D structures, particularly junction structures, from a given 2D structure. Through global sampling of the 3D arrangements of the helices in junctions using molecular dynamics simulations and in explicit consideration of non-canonical base pairing and base stacking interactions as well as long-range loop-loop interactions, the model can provide significantly improved predictions for multibranched junction structures than existing methods. Moreover, integrated with additional restraints from experiments, such as junction topology and long-range interactions, the model may serve as a useful structure generator for various applications.
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