Preprint: https://doi.org/10.1101/2025.11.28.691195
First, install openfold following instructions on this page https://openfold.readthedocs.io/en/latest/Installation.html. Current repo uses this version of openfold https://github.com/aqlaboratory/openfold/releases/tag/v2.2.0.
(Notes from Dec 2025: I needed to remove flash-attn from the environment.yml file to successfully set up the enviroment.)
Then, in the enviroment with openfold, install AF2Dock as follows:
git clone https://github.com/Graylab/AF2Dock.git
cd AF2Dock
pip install .
If you run into issue installing fastpdb (required by pinder), follow instructions on the pinder repo page (https://github.com/pinder-org/pinder) to download the rust toolchain.
Model weights are uploaded to Zenodo (https://doi.org/10.5281/zenodo.17782958). Detailed instructions coming soon.