This is the official Github repo for the following papers:
- Jin et al., DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design, Biorxiv 2023
- Jin et al., Unsupervised protein-ligand binding energy prediction with Neural Euler's Rotation Equations, NeurIPS 2023
The training and test data can be downloaded from https://zenodo.org/records/10402853. Please put the download data in data/ under the root folder.
Please make sure you install the following packages
- pytorch (tested on v1.13)
- biotite (https://www.biotite-python.org/install.html)
- SRU++ (https://github.com/asappresearch/sru)
- ESM-2 (https://github.com/facebookresearch/esm)
- Chemprop (https://github.com/chemprop/chemprop)
- tqdm
- rdkit
- sidechainnet <= 0.7.6 (1.0 changes the side-chain dimension from 14 to 15)
Once you finished these installation, please run pip install -e .. To install SRU++, run
git clone https://github.com/asappresearch/sru
cd sru
git checkout 3.0.0-dev
pip install .
This notebook tutorials.ipynb contains all the relevation information on predicting binding energy for protein-ligand, protein-protein, and antibody-antigen complexes.