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 and simulation of coarse-grained (CG) membrane protein systems. We have also included a comparison to an equivalent all-atom (AA) simulation in order to raise awareness of where each has merit.
We have separated the content into 5 conceptually distinct parts:
- Construction of an AA membrane protein system
- Simulation/Visualisation of the AA system
- Construction of a CG membrane protein system
- Equilibration of the CG system
- Analysis of protein function and membrane dynamics
The user should work sequentially through each numbered directory within this repo
starting from 1-allatom_setup and finishing with 5-coarsegrain_analysis
We acknowledge the work published by the Vanni lab which inspired the topic of this practical:
Lipid scrambling is a general feature of protein insertases
Li D., Rocha-Roa C., Schilling M.A., Vanni S.
https://www.pnas.org/doi/10.1073/pnas.2319476121
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/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:
- Robert Clark
- Iain Peter Shand Smith
Please direct all questions and feedback to Robert Clark or Iain Peter Shand Smith