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 in it.

conda activate colabdock && python main.py

If you want to test ColabDock using a complex with known structure, you can generate 1v1, 1vN, or MvN restraints using the extract_rest.py script. For example, 4INS4 contains 4 protein chains, i.e., A,B,C,D. If you want to sample some 1v1 restraints between chain A and chain D, then run the following command and the program will print the sampled restraints.

python extract_rest.py ./protein/4INS4/PDB/native.pdb A,B,C,D A,D 1v1

You can also use python extract_rest.py -h to get more informations about the input parameters.

Suppose the complex you want to dock contains two chains, i.e., A and B, and each chain contains 10 amino acids. The "chains" variable in the config.py file is set to 'A,B'.

If you want the 4th residue in chain A close to the 5th residue in chain B in the docking structure, the 1v1 restraint (rest_1v1 variable in the config.py file) should be set to [4, 15].

If you want the 4th residue in chain A close to one of residues from 3rd to 7th in chain B in the docking structure, the 1vN restraint (rest_1vN variable in the config.py file) should be set to [4, range(13, 18)].

If you have two 1vN restraints, i.e., [4, range(13, 18)] and [6, range(13, 18)], and you want at least one of them satisfied in the docking structure, the MvN restraint (rest_MvN variable in the config.py file) should be set to [[4, range(13, 18)], [6, range(13, 18)], 1].

If you want the 6th residue in chain A far away from the 8th residue in chain B in the docking structure, the repulsive restraint (rest_rep variable in the config.py file) should be set to [6, 18].

A blog in Chinese (link)

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