DeepCoSI: a Structure-based Deep Graph Learning Network Method for Covalent Binding Site Identification.
# software
chimera v1.13.1
# python
python 3.6.13
# environment to reproduce
conda env create -f DeepCoSI.yml
nohup python -u ./codes/DeepCoSI_Train.py --gpuid 0 &
In order to speed up the calculation, we only used a small part of the data as an example.
We provide a well-trained model for users to predict the ligandability of cysteine.
# example
python ./codes/DeepCoSI_prediction.py 4hqr.pdb example
# Please check the prediction result in the build directory.
We profiled the structures in RCSB PDB to identify potential cysteines for covalent ligand discovery. Please use it in http://cadd.zju.edu.cn/cidb/deepcosi/cys.
@article{
doi:10.34133/2022/9873564,
author = {Hongyan Du and Dejun Jiang and Junbo Gao and Xujun Zhang and Lingxiao Jiang and Yundian Zeng and Zhenxing Wu and Chao Shen and Lei Xu and Dongsheng Cao and Tingjun Hou and Peichen Pan },
title = {Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network},
journal = {Research},
volume = {2022},
number = {},
pages = {},
year = {2022},
doi = {10.34133/2022/9873564},
URL = {https://spj.science.org/doi/abs/10.34133/2022/9873564},
eprint = {https://spj.science.org/doi/pdf/10.34133/2022/9873564},
}