This repository contains all the materials for the Simulation of Biomolecules Advanced course, part of the CCP5 Summer School taking place on 29-31 July 2025 at Newcastle University. The materials are taken from the CCPBioSim course BioSim-analysis-workshop.
- Dr Matteo Degiacomi, University of Edinburgh (MTD)
- Dr Daniel Cole, Newcastle University (DC)
- Jasmin Güven, University of Edinburgh (JG)
L1-8: Lectures. P: practical.
| 29 July | Session | Materials |
|---|---|---|
| 09:00-10:00 | L1: Introduction to Proteins (MTD) | 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 | Lecture Slides |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:00 | Simulation Setup continued (DC) |  |
| 15:00-15:30 | L5 Simulation Basic Analyses (MTD) | Lecture Slides |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | L5 & P: Simulation Basic Analyses (MTD) | Lecture Slides, |
| 30 July | Session | Materials |
|---|---|---|
| 09:00-11:00 | L6: Dimensionality Reduction (MTD), P: Dimensionality Reduction (MTD) | Lecture Slides , |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L7 & P: Clustering (MTD) | Lecture Slides, |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:30 | L4 & P: Protein-Ligand Docking (DC) | Lecture Slides, |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | L4 & P: Protein-Ligand Docking, contd. (DC) |
| 31 July | Session | Materials |
|---|---|---|
| 09:00-10:00 | L8: Data Classification (MTD) | Lecture Slides |
| 10:00-11:00 | P: Data Classification (MTD) | |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | P: Q&A on previous practicals | |
| 12:30-14:00 | Lunch | 🍝 |
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.