This workshop source repository contains the build recipe for a docker container derived from the CCPBioSim JupyterHub image. This container adds the necessary software packages and notebook content to form a deployable course container.
This workshop walks through the process of preparing a simple protein system for molecular dynamics simulation using Ambertools. In addition, it showcases the use of Alphafix to remediate crystal structure-derived models (identify and rebuild missing atoms and residues).
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/protein-preparation-workshop:latest
In our containers we are using the JupyterHub default port 8888, so you should forward this port when deploying locally::
docker run -p 8888:8888 ghcr.io/ccpbiosim/protein-preparation-workshop:latest
Workshop Content Authors:
- Charlie Laughton
Please direct all questions and feedback to Charlie Laughton