Update: This repository is still in progress.
In our paper, we introduce a LLM-based agent for drug discovery called LIDDiA (Language-based Intelligent Drug Discovery Agent). Using LIDDiA, you can specify what properties the molecules should have, and LIDDiA will run computational tools to generate and evaluate the molecules.
Note: The current code for LIDDiA randomly sample molecules from TDC ZINC rather than using Pocket2Mol
The environment dependencies for conda is available in environment.yml.
You need to set up an Anthropic API key and put it in my-anthropic-key.txt to run the command.
python run.py --target EGFR --max_iter 10 --model "claude-3-5-sonnet-20241022"The argument for --target must be one of the targets in dataset/pdb/. The list of arguments for --model is available here.
If you use the code in this repository, please cite with the following BibTeX entry:
@article{averly2025liddia,
title={Liddia: Language-based intelligent drug discovery agent},
author={Averly, Reza and Baker, Frazier N and Watson, Ian A and Ning, Xia},
journal={arXiv preprint arXiv:2502.13959},
year={2025}
}
If you use the dataset in this repository, please cite the following works as well:
@article{gaulton2012chembl,
title={ChEMBL: a large-scale bioactivity database for drug discovery},
author={Gaulton, Anna and Bellis, Louisa J and Bento, A Patricia and Chambers, Jon and Davies, Mark and Hersey, Anne and Light, Yvonne and McGlinchey, Shaun and Michalovich, David and Al-Lazikani, Bissan and others},
journal={Nucleic acids research},
volume={40},
number={D1},
pages={D1100--D1107},
year={2012},
publisher={Oxford University Press}
}
@article{burley2019rcsb,
title={RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy},
author={Burley, Stephen K and Berman, Helen M and Bhikadiya, Charmi and Bi, Chunxiao and Chen, Li and Di Costanzo, Luigi and Christie, Cole and Dalenberg, Ken and Duarte, Jose M and Dutta, Shuchismita and others},
journal={Nucleic acids research},
volume={47},
number={D1},
pages={D464--D474},
year={2019},
publisher={Oxford University Press}
}
Please send an email to averly.1@buckeyemail.osu.edu