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.
Here we present a practical introduction to the construction, simulation and analysis of coarse-grained (CG) membrane protein system.
We have separated the content into tutorial notebooks:
- Preparing a protein with Martini 3
- Building the system (with a membrane)
- Preparing for production simulation
- Analysis of the simulation
- Conversion to atomistic resolution
The user should work sequentially through each numbered directory within this repository, starting from tutorial_1
This tutorial is inspired by the previous Coarse-graining workshop, run by Robert Clark and Iain Peter Shand Smith, in combination with those found on the Martini tutorial section.
The work that inspired the system studied in these tutorials can be found here:
Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2. Sebastian Bieker, Michael Timme, Nils Woge, Dina G. Hassan, Chelsea M. Brown, Siewert J. Marrink, Manuel N. Melo & Joost C. M. Holthuis https://doi.org/10.1038/s42003-025-07551-9
This training course is deployed on the CCPBioSim website via our cloud infrastructure, however you can deploy it on your own machine with docker.
Pull the container from our repository::
docker pull ghcr.io/ccpbiosim/coarse-graining-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/coarse-graining-workshop:latest
Workshop Content Authors:
Please direct all questions and feedback to Chelsea M. Brown (chelsea.m.brown[at]warwick.ac.uk)