ColabDock is a docking framework developed based on ColabDesign. It is able to incorporate experimental restraints to generate accurate protein complex structure. For details, please refer to the paper.

Note the notebook is still under development.

1. Create a python enviroment using conda.

conda create --name colabdock python=3.8

2. Clone the repo

git clone [email protected]:JeffSHF/ColabDock.git

3. Activate environment

cd ColabDock && conda activate colabdock

4. Install jax
   Please refer to JAX github page to install package corresponding to your CUDA and cudnn version.
   Example:

# install jaxlib
pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.8+cuda11.cudnn805-cp38-none-manylinux2014_x86_64.whl
# install jax
pip install jax==0.3.8

4. Install other dependencies

pip install -r requirements.txt

Before running the code, please set the variables in the config.py file according to the descriptive information.

conda activate colabdock && python main.py

• Shihao Feng @JeffSHF
• Zhenyu Chen @Dreams1de
• Sergey Ovchinnikov @sokrypton