⛰️ Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction (ICLR 2023)
conda env create -f env.yml -n RDE
conda activate RDEThe default PyTorch version is 1.12.1 and cudatoolkit version is 11.3. They can be changed in env.yml.
| Dataset | Download Script |
|---|---|
| PDB-REDO | data/get_pdbredo.sh |
| SKEMPI v2 | data/get_skempi_v2.sh |
https://drive.google.com/drive/folders/1jS7VCLyLZoxDyYb092Y7QqxyOGUE8iUm?usp=share_link
python test_rde_network_skempi.py --ckpt ./trained_models/DDG_RDE_Network_30k.ptpython test_rde_linear_skempi.py --ckpt ./trained_models/RDE.pt
python pointmut_analysis.py ./configs/inference/7FAE_RBD_Fv_mutation.yml💡 The script can also predict mutational effects for other protein complexes. Please refer to the example configuration file 7FAE_RBD_Fv_mutation.yml to create your own mutation instruction.
python train.py ./configs/train/rde.ymlpython train_rde_network_skempi.py ./configs/train/rde_ddg_skempi.yml@inproceedings{luo2023rotamer,
title={Rotamer Density Estimator is an Unsupervised Learner of the Effect of Mutations on Protein-Protein Interaction},
author={Shitong Luo and Yufeng Su and Zuofan Wu and Chenpeng Su and Jian Peng and Jianzhu Ma},
booktitle={The Eleventh International Conference on Learning Representations },
year={2023},
url={https://openreview.net/forum?id=_X9Yl1K2mD}
}
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