# Module 3: The Architect

> Understand how secondary structures pack into domains and tertiary structure.

Global Folding

Understand how secondary structures pack into domains and tertiary structure.

- Explain why the hydrophobic core is the primary thermodynamic driving force for folding
- Judge packing quality and recognise cavities as a destabilising defect
- Apply the geometric requirements for a viable disulfide bond
- Diagnose buried charges and exposed hydrophobic patches from a residue distribution
- Identify domain boundaries and explain why they matter for redesign
- Repair several independent structural defects in one protein and predict the consequences

## Links

- [Introduction](https://proteindesign.academy/module/3/intro)
- [3.1 Building the Hydrophobic Core](https://proteindesign.academy/module/3/1)
- [3.2 Disulfide Bridges](https://proteindesign.academy/module/3/2)
- [3.3 Surface vs Buried: The Inside-Out Rule](https://proteindesign.academy/module/3/3)
- [3.4 Domain Architecture](https://proteindesign.academy/module/3/4)
- [3.integration The Protein Repair Shop](https://proteindesign.academy/module/3/integration)
- [The Folding Architect](https://proteindesign.academy/module/3/capstone)
- [Start Here](https://proteindesign.academy/start-here)
- [Tools & Papers](https://proteindesign.academy/tools-and-papers)
- [Continuing Practice](https://proteindesign.academy/continuing-practice)