CCPBioSim Ubiquitin Analysis Workshop

This workshop illustrates the application of a number of Python-based tools to the analysis of the results from a short (1 nanosecond) simulation of ubiquitin, investigating the question "how similar is the MD trajectory to the crystal and NMR structures?"

The workshop illustrates:

1. The use of the Python MDTraj module (see http://www.mdtraj.org)
2. The use of the Python matplotlib module for plotting (see http://www.matplotlib.org)
3. The use of the Python MDPlus module for Principal Component Analysis (see http://bitbucket.org/claughton/mdplus)

Docker

This container is derived from the CCPBioSim JupyterHub base image. This container adds the necessary software packages and notebook content to form a deployable course container.

How to Use

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/ubiquitin-analysis-workshop:latest

Contact

Please direct all comments and queries to Charlie Laughton