AIMEE

This repo contains code and data for manuscript "A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe" published in Briefing in Bioinformatics, 2021. (https://doi.org/10.1093/bib/bbab301)

Reqirements:

• Pytorch=1.2.0
• torchvision=0.4.0
• cudatoolkit=10.0 (View version: cat /usr/local/cuda/version.txt)
• Python3
• Rdkit
• transformers=2.7.0 (How to install: huggingface/transformers)

(1) Transformer pretrained model (for protein sequence)

• We use a large number of protein sequence data to pre train a modified transformer model, which is saved in the path ./pretrained_model/pytorch_model.pth.
• The configuration of the model is saved in the path ./pretrained_model/bert_config.json.

(2) GAT (for protein structure)

• The relevant files of this model are saved in the directory ./AttentiveFP.

(3) GAT (for molecular graph)

• The relevant files of this model are saved in the directory ./ProEmb, meanwhile, other models of proteins are also saved in this directory.

Usage:

The entry of the whole program is in the main.py. It includes the selection of input and output files and the definition of parameters. It can run directly by python main.py.

Use agreement

The SOFTWARE will be used for teaching or not-for-profit research purposes only. Permission is required for any commerical use of the Software.