RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA–protein binding sites prediction
Abstract RNA-binding proteins (RBPs) play crucial roles in gene regulation. Their dysregulation has been increasingly linked to neurodegenerative diseases, liver cancer, and lung cancer. Although experimental methods like CLIP-seq accurately identify RNA–protein binding sites, they are time-consumin...
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| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-07-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-025-06197-y |
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| Summary: | Abstract RNA-binding proteins (RBPs) play crucial roles in gene regulation. Their dysregulation has been increasingly linked to neurodegenerative diseases, liver cancer, and lung cancer. Although experimental methods like CLIP-seq accurately identify RNA–protein binding sites, they are time-consuming and costly. To address this, we propose RMDNet—a deep learning framework that integrates CNN, CNN-Transformer, and ResNet branches to capture features at multiple sequence scales. These features are fused with structural representations derived from RNA secondary structure graphs. The graphs are processed using a graph neural network with DiffPool. To optimize feature integration, we incorporate an improved dung beetle optimization algorithm, which adaptively assigns fusion weights during inference. Evaluations on the RBP-24 benchmark show that RMDNet outperforms state-of-the-art models including GraphProt, DeepRKE, and DeepDW across multiple metrics. On the RBP-31 dataset, it demonstrates strong generalization ability, while ablation studies on RBPsuite2.0 validate the contributions of individual modules. We assess biological interpretability by extracting candidate binding motifs from the first-layer CNN kernels. Several motifs closely match experimentally validated RBP motifs, confirming the model’s capacity to learn biologically meaningful patterns. A downstream case study on YTHDF1 focuses on analyzing interpretable spatial binding patterns, using a large-scale prediction dataset and CLIP-seq peak alignment. The results confirm that the model captures localized binding signals and spatial consistency with experimental annotations. Overall, RMDNet is a robust and interpretable tool for predicting RNA–protein binding sites. It has broad potential in disease mechanism research and therapeutic target discovery. The source code is available https://github.com/cskyan/RMDNet . |
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| ISSN: | 1471-2105 |