Module
Structure prediction
Obtaining a 3D structure when no experimental structure is available: AlphaFold, homology modelling and model quality assessment.
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
- Choose a structure prediction method suited to your case
- Run AlphaFold or ESMFold and interpret the results
- Read and critically assess pLDDT and PAE scores
- Build a homology model and validate its quality
- Prepare a predicted model for molecular docking
Day 1 — Foundations and preparation
| Time | Content | Type |
|---|---|---|
| 09:00 – 09:30 | Welcome, introduction of participants and objectives | Introduction |
| 09:30 – 10:45 | Theory: the protein folding problem and its computational approaches | Theory |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | AlphaFold2 and ESMFold: using the online servers | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Reading pLDDT and PAE scores: what is reliable and what is not | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 17:15 | Practical case: predicting a target with no experimental structure | 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 | Homology modelling: principles and when to use it | Theory |
| 10:00 – 10:45 | Template selection and alignment with MODELLER or SWISS-MODEL | Practical work |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | Model validation: Ramachandran plot, Z-score, ERRAT | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Repairing and preparing the model for docking | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 16:45 | Comparing predicted and experimental structures | Practical work |
| 16:45 – 17:30 | Final assessment and closing | Wrap-up |
Prerequisites
- Basic structural biochemistry
- Basic structural biochemistry
- No programming experience required
Required equipment
- Computer with at least 8 GB RAM
- Linux, macOS or Windows 10+
- Stable internet connection
- Software provided: AutoDock Vina, MGLTools, PyMOL
Interested in this module?
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