This repository contains the materials for day 1 and 3 of the Simulation of Biomolecules Advanced course, part of the CCP5 Summer School taking place on 28th-30th July 2026 at Newcastle University. The materials are taken from the CCPBioSim course BioSim-analysis-workshop. Day 2 materials will be provided separately.
- Dr Finlay Clark, Newcastle University (FC)
- Dr Daniel Cole, Newcastle University (DC)
- Dr Jasmin Güven, University of Bristol (JG)
The content in this workshop was created by:
- Dr Matteo Degiacomi, University of Edinburgh
- Dr Antonia Mey, University of Edinburgh
- Dr Daniel Cole, Newcastle University
L1-8: Lectures. P: practical.
| 28 July | Session | Materials |
|---|---|---|
| 09:00-10:00 | L1: Introduction to Proteins (DC) | Lecture Slides |
| 10:00-11:00 | L2: Understanding Protein Systems (JG) | Lecture Slides |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:00 | P: Understanding Complex Protein Systems, contd. (JG) | Webserver |
| 12:00-12:30 | L3 Simulation Setup (FC) | Lecture Slides |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:00 | P: Simulation Setup continued (FC) |  |
| 15:00-15:30 | L5 Simulation Basic Analyses (JG) | Lecture Slides |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | L5 & P: Simulation Basic Analyses (JG) | Lecture Slides, |
| 30 July | Session | Materials |
|---|---|---|
| 09:00-11:00 | L4 & P: Protein-Ligand Docking (DC) | Lecture Slides, |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L4 & P: Protein-Ligand Docking, contd. (DC) |
These are additional materials on machine learning methods used in biomolecular simulations that you can go through in your own time:
| Session | Materials |
|---|---|
| L6: Dimensionality Reduction, P: Dimensionality Reduction | Lecture Slides, , |
| L7 & P: Clustering | Lecture Slides, |
| L8: Data Classification, P: Data Classification | Lecture Slides, |
The workshop is designed to run on Google Colab, and all workshop notebooks run directly from your browser; no installation is required. In particular, please note that the Open Force Field material in the Jupyter notebook of session 4_Simulation_Setup will not natively run on Windows machines. For extra information, see here](https://docs.openforcefield.org/en/latest/install.html#openff-on-windows).
Instructions for setting up your environment to run this workshop locally are provided in INSTALL.md.
A full list of the required Python packages can be seen inside environment.yml.
To avoid waiting for everyone's setup to be up and running, we highly recommend trying this workshop on Colab and only once you are back at home and want to explore further to try and run it on your local machine.
The course assumes that attendees have a working knowledge of Jupyter notebooks, Python (especially the NumPy library), and the bash shell.
- The MDAnalysis logo and its derivatives are licensed under the Creative Commons Attribution-NoDerivs 3.0 Unported License.
- The MDAnalysis material in folder 5_* is licenced under CC-BY 4.0
- The Docking material in folder 3_* is licensed under and Apache-2.0 and MIT license.
- The Open Force Field material in folder 4_* is licensed under MIT license.
- Material in folders 1_*,
2_*,
6_*,
7_*
8_*, and
9_* is licenced under CC-BY-SA 4.0.
Please see AUTHORS.md for a list of contributors to the workshop materials.