ArticleNucleic acids research2017
Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- APDB: A Large-Scale Repository of Predicted 2D and 3D Aptamer Structures.Journal of chemical information and modeling · 2026Article
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- R3J-AGNN: GNN-Based Prediction of Inter-Branch Angles in RNA Three-Way Junctions from Secondary Structure.Biology · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
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- piR-RCC Suppresses Renal Cell Carcinoma Progression by Facilitating YBX-1 Cytoplasm Localization.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Predicting RNA Structure Utilizing Attention from Pretrained Language Models.Journal of chemical information and modeling · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Autonomous Nucleic Acid and Protein Nanocomputing Agents Engineered to Operate in Living Cells.ACS nano · 2025Review
- miRVim: Three-dimensional miRNA Structure Database.MicroRNA (Shariqah, United Arab Emirates) · 2025Article
- AI-integrated network for RNA complex structure and dynamic prediction.Biophysics reviews · 2024Review
- 3dDNAscoreA: A scoring function for evaluation of DNA 3D structures.Biophysical journal · 2024Article
- Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.Nature methods · 2024Article
- trRosettaRNA: automated prediction of RNA 3D structure with transformer network.Nature communications · 2023Article
- Stress-enhanced cardiac lncRNA Morrbid protects hearts from acute myocardial infarction.JCI insight · 2023Article
- RNA 3D Structure Prediction: Progress and Perspective.Molecules (Basel, Switzerland) · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Role of RNA Domain Structure and Orientation in the Coxsackievirus B3 Virulence Phenotype.Journal of virology · 2023Article
- cgRNASP: coarse-grained statistical potentials with residue separation for RNA structure evaluation.NAR genomics and bioinformatics · 2023Article
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Direct coupling analysis of nucleotide coevolution provides a novel approach to identify which nucleotides in an RNA molecule are likely in direct contact, and this information obtained from sequence only can be used to predict RNA 3D structures with much improved accuracy. Here we present an efficient method that incorporates this information into current RNA 3D structure prediction methods, specifically 3dRNA. Our method makes much more accurate RNA 3D structure prediction than the original 3dRNA as well as other existing prediction methods that used the direct coupling analysis. In particular our method demonstrates a significant improvement in predicting multi-branch junction conformations, a major bottleneck for RNA 3D structure prediction. We also show that our method can be used to optimize the predictions by other methods. These results indicate that optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis offers an efficient way for accurate RNA tertiary structure predictions.
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