Module
Molecular docking
Principles of docking, receptor and ligand preparation, search grid definition, AutoDock Vina parameterisation and interpretation of affinity scores.
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
- Explain the principles of docking and the limitations of scoring functions
- Prepare a receptor and a ligand in PDBQT format
- Select an active site and define a relevant search grid
- Parameterise AutoDock Vina according to the biological question
- Validate a protocol by redocking and interpret the RMSD
Day 1 — Foundations and preparation
| Time | Content | Type |
|---|---|---|
| 09:00 – 09:30 | Welcome, introduction of participants and objectives | Introduction |
| 09:30 – 10:45 | Theory: protein-ligand interactions (hydrogen, hydrophobic, electrostatic, π-stacking) | Theory |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | Scoring functions: principles, strengths and limitations. Why the score is not a free energy | Theory |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Receptor preparation: PDB cleaning, adding hydrogens, handling waters and cofactors | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 17:15 | PDB → PDBQT conversion with AutoDockTools and MGLTools. Ligand preparation | 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 | Review of day 1. Active site identification: experimental structures, prediction, literature | Theory |
| 10:00 – 10:45 | Search grid definition: centre, dimensions, allosteric site cases | Theory |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | Vina parameterisation: exhaustiveness, num_modes, energy_range. Effect on computation time and results | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Running the docking. Reading the output file and affinity scores | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 16:45 | Validation by redocking: RMSD calculation between predicted and crystallographic pose | Practical work |
| 16:45 – 17:30 | Interpreting results, common pitfalls, final assessment and closing | Wrap-up |
Prerequisites
- Basic biochemistry, command line
- Basic knowledge of protein structure
- No programming experience required
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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