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Prompt-DDG

Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning

Lirong Wu, Yijun Tian, Haitao Lin, Yufei Huang, Siyuan Li, Nitesh V Chawla, Stan Z. Li. In ICML, 2024.

Dependencies

conda env create -f environment.yml
conda activate Prompt-DDG

The default PyTorch version is 1.8.1 and cudatoolkit version is 11.3. They can be changed in environment.yml.

Dataset

Dataset Download Script
SKEMPI v2 data/get_skempi_v2.sh

Usage

Codebook Pre-training and DDG Prediction

python -B train.py

The customized hyperparameters are available in ./configs/param_config.json.

Loading the Pre-trained Model and Making Inference

We provide a pre-trained model in Google Drive for DDG prediction on SKEMPI v2. To use it, please download it to ./trained_models/ and run

python -B train.py --ckpt_path ../trained_models/ddg_model.ckpt

Citation

If you are interested in our repository and our paper, please cite the following paper:

@article{wu2024learning,
  title={Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning},
  author={Wu, Lirong and Tian, Yijun and Lin, Haitao and Huang, Yufei and Li, Siyuan and Chawla, Nitesh V and Li, Stan Z},
  journal={arXiv preprint arXiv:2405.10348},
  year={2024}
}

@article{wu2024mape,
  title={MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding},
  author={Wu, Lirong and Tian, Yijun and Huang, Yufei and Li, Siyuan and Lin, Haitao and Chawla, Nitesh V and Li, Stan Z},
  journal={arXiv preprint arXiv:2402.14391},
  year={2024}
}

Feedback

If you have any issue about this work, please feel free to contact me by email: