Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence

Paola Ruiz Puentes, Maria C. Henao, Javier Cifuentes, Carolina Muñoz-Camargo, Luis H. Reyes, Juan C. Cruz and Pablo Arbeláez.

This repository contains the official implementation of AMPs-Net: Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence.

Paper

Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence.
Paola Ruiz Puentes^1,2, Maria C. Henao³, Javier Cifuentes², Carolina Muñoz-Camargo²,Luis H. Reyes³, Juan C. Cruz², Pablo Arbeláez¹
Membranes MDPI, 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.
³ Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de los Andes, Bogota 111711, Colombia.

Installation

The following steps are required in order to run AMPs-Net:

$ export PATH=/usr/local/cuda-11.0/bin:$PATH 
$ export LD_LIBRARY_PATH=/usr/local/cuda-11.0/lib64:$LD_LIBRARY_PATH 

$ conda create --name amps_env 
$ conda activate amps_env 

$ bash amps_env.sh

Models

We provide pretrained models available for download in the following link. Last update on the models on the 01/01/2023.

Usage

To train each of the components of our method: please refer to run_AMP.sh and run_multilabel.sh.

To perform inference on your data please refer to: run_inference_AMP.sh and run_inference_multilabel.sh.

To setup your data on the proper format for our models please refer to generate_metadata.sh. Your dataset should be a csv file with a column name Sequence and your peptides in their AA sequence. Follow the example in data/datasets/Inference.

To perform inference with your models please modify L34-37 from inference.py. (Change Checkpoint.pth to Checkpoint__valid_best.pth)

Citation

We hope you find our paper useful. To cite us, please use the following BibTeX entry:

@article{RuizPuentes2022,
  doi = {10.3390/membranes12070708},
  url = {https://doi.org/10.3390/membranes12070708},
  year = {2022},
  month = jul,
  publisher = {{MDPI} {AG}},
  volume = {12},
  number = {7},
  pages = {708},
  author = {Paola Ruiz Puentes and Maria C. Henao and Javier Cifuentes and Carolina Mu{\~{n}}oz-Camargo and Luis H. Reyes and Juan C. Cruz and Pablo Arbel{\'{a}}ez},
  title = {Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence},
  journal = {Membranes}
}