A workflow that runs fred
or diffdock
to screen small molecules for receptor proteins. The program can be run as a local script or a colmena
workflow.
We will set up the run environment with Anaconda/Miniconda.
The base environment can be setup with the env.yml
file in the repo.
git clone https://github.com/hengma1001/bvbrc_docking.git
cd bvbrc_docking
conda env create -n bvbrc_docking -f env.yml
pip install .
The required torch
modules are installed using pip
. It's recommand the user download the correct CUDA version for pytorch
. (Note: test the pyg with conda install to reduce compilation time. )
pip install torch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0
pip install torch-scatter==2.1.2 torch-sparse==0.6.18 torch-cluster==1.6.3 torch-geometric==2.4.0
Next we need to setup DiffDock
, along with esm
. The Diffdock uses the esm
package to obtain protein embeddings and structures.
git clone https://github.com/gcorso/DiffDock.git
cd DiffDock
git checkout a6c527536d286a693d1d6f9fc97142506ef76179
git clone https://github.com/facebookresearch/esm
cd esm
git checkout ca8a710
python -m bvbrc_docking.run_local -c runs/fred_local.yml