https://github.com/lirongwu/prompt-ddg

Code for ICML 2024 paper "Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning"
https://github.com/lirongwu/prompt-ddg

antibody-optimization mutational-effect-prediction prompt-leaning protein-protein-interaction

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Code for ICML 2024 paper "Learning to Predict Mutational Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning"

• Host: GitHub
• URL: https://github.com/lirongwu/prompt-ddg
• Owner: LirongWu
• License: mit
• Created: 2024-05-06T19:26:37.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2024-06-26T11:03:22.000Z (5 months ago)
• Last Synced: 2024-09-05T15:50:46.591Z (2 months ago)
• Topics: antibody-optimization, mutational-effect-prediction, prompt-leaning, protein-protein-interaction
• Language: Python
• Homepage:
• Size: 17.8 MB
• Stars: 27
• Watchers: 3
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://openreview.net/forum?id=g89jAdrnAF), 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](https://life.bsc.es/pid/skempi2) | [`data/get_skempi_v2.sh`](./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](https://drive.google.com/file/d/10Cqp42Q-hp2Dm0278EdpCfvKpMKBeiu_/view?usp=sharing) 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: 

* Lirong Wu: [email protected]