README.md

metadata

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

DrugGPT

A generative drug design model based on GPT2.

Deployment

1. Clone

   git lfs install
   git clone https://huggingface.co/liyuesen/druggpt
   

2. Create virtual environment

   conda create -n druggpt python=3.7
   conda activate druggpt
   

3. 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