Alphafold Pipeline

• End to end protein structure prediction pipeline, from seq to pdb.

Docker file

Build docker image from https://github.com/GuanyiLi-Craig/protein-predictor/blob/master/v2/Dockerfile

sudo docker build -t alphafold_pipeline .

Arch

[pic]

Start

1. Move HHBlist database to path-to-this-git-directory/alphafold/database
2. Move sequence data to path-to-this-git-directory/alphafold/data//
3. Start Docker by

sudo docker run -d -p 8888:8888 --gpus all --ipc=host -v <path-to-directory>/alphafold:/data alphafold_pipeline jupyter notebook --no-browser --ip=0.0.0.0 --allow-root --NotebookApp.token= --notebook-dir='/data'