Generative Diffusion Models for Antibody Design, Docking, and Optimization

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Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.

The wet experiment data used to validate our pipeline is available at wet_experiment_data.zip

Quick start

Installation

git clone [email protected]:pengzhangzhi/ab_opt.git

Antibody optimization pipeline

want to use it online? Check out the colab version of the antibody optimization pipeline.

Running the pipeline in local

• git clone [email protected]:pengzhangzhi/ab_opt.git
• Go the AbDock
• Follow the README to install the env
• Open notebook ab_opt.ipynb
• specify pdb file which contains an antibody-antigen complex structure
• specify the heavy chain ID and the residue indices to be designed

AbDesign

Please take a look at the AbDesign on reproducing the training and evaluation of the AbDesign.

AbDock

Please refer to the AbDock on how to reproduce the training and evaluation of the AbDock and the antibody optimization pipeline.

Credits

This codebase is based on the following repositories, we thank the authors for their great work.

• DockQ
• diffab
• Abnumber
• PyRosetta
• ...