Learning Structure-based Pocket Representations for Protein-Ligand Interaction Prediction.
Please refer to our Cell Systems paper for more detailed information.
Cite our paper by
@article{li2022pocketanchor,
title={PocketAnchor: Learning Structure-based Pocket Representations for Protein-Ligand Interaction Prediction},
author={Li, Shuya and Tian, Tingzhong and Zhang, Ziting and Zou, Ziheng and Zhao, Dan and Zeng, Jianyang},
journal={Cell Systems},
volume={14},
number={8},
pages={692-705.e6},
year={2023},
issn={2405-4712},
doi={https://doi.org/10.1016/j.cels.2023.05.005},
url={https://www.sciencedirect.com/science/article/pii/S2405471223001497},
}
The code for data processing can be found in https://github.com/lishuya17/PocketAnchorData.
The processed data can be found in docker image: https://hub.docker.com/r/tiantz17/pocketanchor-models. (Not recommended)
(Update) You can pull another docker image containing code, data, environment, trained models, and prediction results for reproduction: https://hub.docker.com/r/tiantz17/pocketanchor.
cuda 11.2
python 3.7.4
torch 1.7.1
torch-geometric 1.6.3
numpy 1.19.0
pandas 1.2.4
rdkit 2020.03.3.0
scikit-learn 0.21.3
scipy 1.6.3
tensorboard 2.4.1
[TASK]/results/[FOLDER]/
.Protein ligand binding site prediction
python runPrediction.py --task PocketDetection --dataset COACH420
python runPrediction.py --task PocketDetection --dataset HOLO4k
Protein-ligand binding affinity prediction
python runPrediction.py --task Affinity --dataset CASF --setting original --info original
python runPrediction.py --task Affinity --dataset CASF --setting newprotein --info newprotein
python runPrediction.py --task Affinity --dataset CASF --setting expanded --info expanded
[TASK]/models/[FOLDER]
.Protein ligand binding site prediction
python runTrain.py --task PocketDetection --dataset scPDB
Protein-ligand binding affinity prediction
python runTrain.py --task Affinity --dataset CASF --setting original --info original
python runTrain.py --task Affinity --dataset CASF --setting newprotein --info newprotein