PLA-Net: Predicting Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery
Paola Ruiz Puentes, Laura Rueda-Gensini, Natalia Valderrama, Isabela Hernández, Cristina González, Laura Daza, Carolina Muñoz-Camargo, Juan C. Cruz, Pablo Arbeláez
This repository contains the official implementation of PLA-Net: Predicting target–ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery.
Predicting target–ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery,
Paola Ruiz Puentes1,2, Laura Rueda-Gensini1,2, Natalia Valderrama1,2, Isabela Hernández1,2, Cristina González1,2, Laura Daza1,2, Carolina Muñoz-Camargo2, Juan C. Cruz2, Pablo Arbeláez1
Scientific Reports, 2022.
1 Center for Research and Formation in Artificial Intelligence .(CINFONIA), Universidad de los Andes, Bogotá 111711, Colombia.
2 Department of Biomedical Engineering, Universidad de los Andes, Bogotá 111711, Colombia.
The following steps are required in order to run PLA-Net:
$ export PATH=/usr/local/cuda-11.0/bin:$PATH <br />
$ export LD_LIBRARY_PATH=/usr/local/cuda-11.0/lib64:$LD_LIBRARY_PATH <br />
$ conda create --name PLA-Net <br />
$ conda activate PLA-Net <br />
$ bash env.shWe provide trained models available for download in the following link.
To train each of the components of our method: LM, LM+Advs, LMPM and PLA-Net please refer to planet.sh file and run the desired models.
To evaluate each of the components of our method: LM, LM+Advs, LMPM and PLA-Net please run the corresponding bash file in the inference folder.
For docker installation you can use the setup in here.
We hope you find our paper useful. To cite us, please use the following BibTeX entry:
@article{ruiz2022predicting,
title={Predicting target--ligand interactions with graph convolutional networks for interpretable pharmaceutical discovery},
author={Ruiz Puentes, Paola and Rueda-Gensini, Laura and Valderrama, Natalia and Hern{\'a}ndez, Isabela and Gonz{\'a}lez, Cristina and Daza, Laura and Mu{\~n}oz-Camargo, Carolina and Cruz, Juan C and Arbel{\'a}ez, Pablo},
journal={Scientific reports},
volume={12},
number={1},
pages={1--17},
year={2022},
publisher={Nature Publishing Group}
}