This repository contains all the materials for the Simulation of Biomolecules Advanced course, part of the CCP5 Summer School taking place on July 23-25th 2024 at Newcastle University.
L1-8: Lectures. P: practical.
| 23th July | Session | Materials |
|---|---|---|
| 09:00-10:00 | L1: Introduction to Proteins (MTD) | Lecture Slides |
| 10:00-11:00 | L2: Understanding Protein Systems (AM) | Lecture Slides |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | P: Understanding Protein Systems, contd. (MTD/AM) | Webserver |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-15:30 | L4 & P: Protein-Ligand Docking (AM) | Lecture Slides,  |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | L4 & P: Protein-Ligand Docking, contd. (AM) |
| 24th July | Session | Materials |
|---|---|---|
| 09:00-11:00 | L3 & P: Simulation Setup (AM/MTD) | Lecture Slides, |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L5 & P: Simulation Basic Analyses (MTD) | Lecture Slides, |
| 12:30-14:00 | Lunch | 🍝 |
| 14:00-14:30 | L6: Dimensionality Reduction (MTD) | Lecture Slides |
| 14:30-15:30 | P: Dimensionality Reduction (MTD/AM) | , |
| 15:30-16:00 | Coffee | ☕ |
| 16:00-17:00 | L7 & P: Clustering (AM) | Lecture Slides, |
| 25th July | Session | Materials |
|---|---|---|
| 09:00-10:00 | L8: Data Classification (MTD) | Lecture Slides |
| 10:00-11:00 | P: Data Classification (MTD/AM) | |
| 11:00-11:30 | Coffee | ☕ |
| 11:30-12:30 | L9: Markov State Modelling (AM) | Lecture Slides |
| 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.
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 Doking 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.