Module
Interaction analysis
Identification and quantification of protein-ligand interactions, pose analysis and result validation. Production of publication-quality figures.
Programme indicatif.
Le déroulé ci-dessous décrit le contenu prévu. Les horaires peuvent être ajustés
selon le rythme du groupe. Aucune date de session n'est encore fixée.
Learning objectives
By the end of this module, you will be able to
- Identify and classify protein-ligand interactions
- Use PLIP to analyse a complex automatically
- Compare poses using interaction fingerprints
- Cluster docking poses to identify representative binding modes
- Produce publication-quality figures
Day 1 — Foundations and preparation
| Time | Content | Type |
|---|---|---|
| 09:00 – 09:30 | Welcome, introduction of participants and objectives | Introduction |
| 09:30 – 10:45 | Theory: types of interactions, geometry, energetic contribution | Theory |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | PLIP: installation and first analysis | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Reading a PLIP report: hydrogen bonds, hydrophobic contacts, π-stacking | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 17:15 | Analysing several complexes and comparing profiles | Practical work |
| 17:15 – 17:45 | Day summary and questions | Wrap-up |
Day 2 — Grid, docking and validation
| Time | Content | Type |
|---|---|---|
| 09:00 – 10:00 | Interaction fingerprints (IFP): principle and use cases | Theory |
| 10:00 – 10:45 | Calculating and comparing IFPs | Practical work |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | Clustering poses: methods and choice of threshold | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Consensus scoring: combining several functions | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 16:45 | PyMOL visualisation and 2D diagram production | Practical work |
| 16:45 – 17:30 | Final assessment and closing | Wrap-up |
Prerequisites
- Module 1
- Basic knowledge of non-covalent interactions
- Having already run a docking
Required equipment
- Computer with at least 8 GB RAM
- Linux, macOS or Windows 10+
- 20 GB free disk space
- Software provided: AutoDock Vina, MGLTools, PyMOL
Interested in this module?
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