RNAFoldDiff-Based Sequence-Aware Graph Diffusion for Accurate RNA 3D Structure Prediction

doi:10.3390/a19050381

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RNAFoldDiff-Based Sequence-Aware Graph Diffusion for Accurate RNA 3D Structure Prediction

2026-05-11

PRE

Abdullah Al-Refai *

Mohammad F. Al-Hammouri

Bandi Vamsi

Ali Al Bataineh *

DOI：10.3390/a19050381

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Abstract

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The prediction accuracy of RNA's tertiary structure remains a core challenge in the field of computational biology. Existing models frequently encounter significant challenges due to the complexities of diverse topologies and the intricate nature of long-range interactions. We introduce RNAFoldDiff, a generative framework that integrates a sequence-aware graph transformer with a geometric diffusion process for end-to-end RNA 3D structure prediction. RNA sequences and secondary structures are converted into graph representations that capture backbone connectivity and base pair topology. The transformer models local motifs and global dependencies, while the diffusion module iteratively denoises coordinates into physically consistent conformations. The model was pretrained on more than 15,000 structural motifs from the RNA 3D Hub and fine-tuned on complete RNAs from the RNA-Puzzles dataset. In benchmarking tests, RNAFold-Diff achieved an average root mean square deviation (RMSD) of 2.64 & Aring;, a Global Distance Test (GDT) score of 68.7%, and a base pair accuracy of 89.5%, reducing RMSD by nearly 30% and improving GDT by 9 points compared to RoseTTAFoldNA. The framework also outperformed FARFAR2, SimRNA, and RNAformer. Ablation experiments confirmed the contributions of diffusion refinement, edge-aware graph encoding, and motif-level pretraining, while qualitative analyses showed biologically plausible folds including helices, junctions, and multiloops. By combining topology-aware graph learning with generative diffusion, RNAFoldDiff advances RNA tertiary structure modeling and provides a practical tool for RNA design, ribozyme analysis, and structure-guided drug discovery.

Keywords:

RNA structure prediction

graph neural networks

geometric deep learning

diffusion models

sequence-aware transformers

3D molecular modeling