metadata

license: artistic-2.0
tags:
  - chemistry
  - biology
  - medical
  - gpt2

DrugGPT

A generative drug design model based on GPT2.

Deployment

Clone
```
git clone https://github.com/LIYUESEN/druggpt.git
cd druggpt
```
Or you can visit our GitHub repo and click Code>Download ZIP to download this repo.

Create virtual environment

conda create -n druggpt python=3.7
conda activate druggpt

Download python dependencies

pip install datasets transformers scipy scikit-learn
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu117
conda install -c openbabel openbabel

Example usage

Run the script with the desired arguments, such as the protein sequence, ligand prompt, number of molecules to generate, and output directory.

If you want to input a protein FASTA file

python drug_generator.py -f bcl2.fasta -n 50

If you want to input the amino acid sequence of the protein

python drug_generator.py -p MAKQPSDVSSECDREGRQLQPAERPPQLRPGAPTSLQTEPQGNPEGNHGGEGDSCPHGSPQGPLAPPASPGPFATRSPLFIFMRRSSLLSRSSSGYFSFDTDRSPAPMSCDKSTQTPSPPCQAFNHYLSAMASMRQAEPADMRPEIWIAQELRRIGDEFNAYYARRVFLNNYQAAEDHPRMVILRLLRYIVRLVWRMH -n 50

If you want to provide a prompt for the ligand

python drug_generator.py -f bcl2.fasta -l COc1ccc(cc1)C(=O) -n 50

License

Artistic License 2.0