/ColabDock

Code for ColabDock paper

Primary LanguagePython

ColabDock

Inverting AlphaFold2 structure prediction model for protein-protein docking with experimental restraints

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.

Open In Colab

Note the notebook is still under development.

Installation

  1. Create a python enviroment using conda.
conda create --name colabdock python=3.8
  1. Clone the repo
git clone git@github.com:JeffSHF/ColabDock.git
  1. Activate environment
cd ColabDock && conda activate colabdock
  1. 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
  1. Install other dependencies
pip install -r requirements.txt

Usage

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

conda activate colabdock && python main.py

Contributors