| <p align="center"> | |
| <img src="https://raw.githubusercontent.com/JulseJiang/RPcontact/main/example/logo.png" alt="RPcontact Logo" width="120"/> | |
| </p> | |
| # RPcontact: RNA-Protein Contact Prediction | |
| **Improved prediction of RNA-protein contacts using RNA and protein language models** | |
| [Paper](https://www.biorxiv.org/content/10.1101/2025.06.02.657171v1.full) | |
| [Code](https://github.com/rpcontact) | |
| [Demo](https://julse-rpcontact.hf.space/) | |
| --- | |
| ## Overview | |
| RPcontact is a novel computational tool for accurately predicting RNA-protein contacts, addressing a fundamental challenge in understanding molecular biology processes such as transcription, splicing, and translation. Traditional methods are limited by the scarcity of RNA-protein complex structures and the constraints of experimental techniques. While recent deep learning approaches like AlphaFold 3 and RoseTTAFoldNA have made progress, they still rely heavily on homologous templates. | |
| RPcontact overcomes these limitations by leveraging large language models specifically designed for RNA ([ERNIE-RNA](https://github.com/Bruce-ywj/ERNIE-RNA)) and proteins ([ESM-2](https://github.com/facebookresearch/esm)). Trained exclusively on ribosomal RNA-protein complexes, RPcontact delivers robust and generalized performance, accurately predicting contacts in both dimeric and multimeric non-rRNA-protein complexes. Benchmark results show that RPcontact significantly outperforms binary contacts inferred from models like AlphaFold 3 and RoseTTAFoldNA, making it a valuable tool for structure and function prediction in RNA-protein research. | |
| --- | |
| ## Quick Start | |
| ### Requirements | |
| | Dependency | Recommended Version | | |
| |-------------|--------------------| | |
| | Python | ≥ 3.8 | | |
| | PyTorch | 1.13.1 | | |
| | fair-esm | 1.0.2 | | |
| Install dependencies (example): | |
| ```bash | |
| pip install numpy pandas matplotlib biopython scikit-learn | |
| pip install torch==1.13.1 | |
| pip install fair-esm==1.0.2 | |
| ``` | |
| --- | |
| ### Script Overview | |
| | Script | Function | Example Command | | |
| |-------------------|-------------------------------------|---------------------------------| | |
| | predict.py | Single RNA-protein pair contact prediction | `python predict.py` | | |
| | predict_batch.py | Batch RNA-protein pairs contact prediction | `python predict_batch.py` | | |
| | evaluate.py | Evaluation and visualization | `python evaluate.py` | | |
| | app.py | Launch web-based demo interface (need install gradio) | `python app.py` | | |
| --- | |
| ### Data Preparation | |
| - RNA/protein sequences: FASTA format | |
| - Embedding features: pickle format | |
| - For batch prediction: provide a CSV file for pairing info | |
| --- | |
| ### Typical Usage | |
| **Single pair prediction:** | |
| ```bash | |
| python predict.py --fasta your_sequence.fasta --out output_dir/ | |
| ``` | |
| **Batch prediction:** | |
| ```bash | |
| python predict_batch.py --rna_fasta rna.fasta --pro_fasta protein.fasta --csv pairs.csv --out output_dir/ | |
| ``` | |
| **Evaluation:** | |
| ```bash | |
| python evaluate.py --fasta your_sequence.fasta --out eval_dir/ --flabel true_labels.pickle | |
| ``` | |
| --- | |
| ### Common Parameters | |
| | Parameter | Description | | |
| |---------------|--------------------------------------------------------| | |
| | --fasta | Input FASTA file (for single prediction) | | |
| | --rna_fasta | RNA FASTA file (for batch prediction) | | |
| | --pro_fasta | Protein FASTA file (for batch prediction) | | |
| | --csv | RNA-protein pairing info CSV (for batch prediction) | | |
| | --ffeat | Precomputed embedding feature file (pickle format) | | |
| | --fmodel | Pretrained model file path | | |
| | --out | Output directory | | |
| | --flabel | True label file (for evaluation) | | |
| | --device | Specify device (e.g., cpu or cuda:0) | | |
| | --draw | Whether to visualize results | | |
| --- | |
| ## Output Interpretation | |
| - The prediction output is a contact probability matrix for each RNA-protein pair. Higher scores indicate a higher probability of interaction. | |
| - The evaluation script provides accuracy and other metrics, as well as visualization. | |
| --- | |
| ## Contact & Citation | |
| Questions or suggestions? Contact: | |
| - Jiuhong Jiang | |
| - Email: jiangjh2023@shanghaitech.edu.cn | |
| If you find this project helpful, please cite our manuscript. | |
| - Jiang, J., Zhang, X., Zhan, J., Miao, Z., & Zhou, Y. (2025). RPcontact: Improved prediction of RNA-protein contacts using RNA and protein language models. bioRxiv, 2025-06. | |
| --- | |
| <p align="center"><em>Make RNA-protein contact prediction easier and more accurate!</em></p> | |