The course is constituted of lectures (L1-8) and practical (P) sessions, subdivided in two units. Unit 1 is dedicated to providing foundations on protein structure and their preparation for MD simulation. Unit 2 is dedicated to describing means of extracting information from the molecular dynamics simulation of a protein.
| Session | Materials |
|---|---|
| L1: Introduction to Proteins | Lecture Slides |
| L2: Understanding Protein Systems | Lecture Slides |
| P: Understanding Protein Systems, contd. | Webserver |
| L3: Protein-Ligand Docking | Lecture Slides |
| P: Protein-Ligand Docking |  |
| L4: Simulation Setup | Lecture Slides |
| P: Simulation Setup | |
| Session | Materials |
|---|---|
| L5: Simulation Basic Analyses | Lecture Slides |
| P: Simulation Basic Analyses | |
| L6: Dimensionality Reduction | Lecture Slides |
| P: Dimensionality Reduction, part 1 | |
| P: Dimensionality Reduction, part 2 | |
| L7: Clustering | Lecture Slides |
| P: Clustering | |
| L8: Data Classification | Lecture Slides |
| P: Data Classification | |
The workshop assumes the participant has a working knowledge of Jupyter notebooks, Python (especially the NumPy library, and the bash shell).
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.
- 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.
