Predicting Antibody–Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants

This repository contains the code, and datasets for our paper.

Repository Overview

This repository is organized as follows:

• Classifiers/: Source code for the implementation of the classifiers described in the paper.
• Data/: Processed dataset used in the experiments (or links to download them).
• Analysis/: Precomputed results, plots, or outputs from the experiments.
• Pretrained LLMs/: Code for pretrained LLMs and training.

Dependencies

To run the code in this repository, you will need:

• Python >= 3.10
• Pytorch

Citation

If you use this code or dataset in your research, please cite:

@article{ashraf2025predicting,
  title={Predicting Antibody--Antigen Interactions with Structure-Aware LLMs: Insights from SARS-CoV-2 Variants},
  author={Ashraf, Faisal Bin and Madrigal, Vinz Angelo and Lonardi, Stefano},
  journal={Journal of Chemical Information and Modeling},
  year={2025},
  publisher={ACS Publications}
}