# Module 9: The Optimizer

> Proteins move. Learn to design for stability across time.

Dynamics & Stability

Proteins move. Learn to design for stability across time.

- Read experimental evidence of protein motion and tell functional flexibility from a structural artefact
- Diagnose stability weak points systematically: cavities, buried charges, unsatisfied hydrogen bonds, exposed patches, mobile loops
- Use the energy landscape to explain what a stabilising mutation actually changes
- Apply the established stabilisation strategies and predict their effect on melting temperature
- Run a full diagnosis-and-repair on a protein while keeping its active site intact

## Links

- [Introduction](https://proteindesign.academy/module/9/intro)
- [9.1 Proteins in Motion](https://proteindesign.academy/module/9/1)
- [9.2 B-Factors and Flexibility](https://proteindesign.academy/module/9/2)
- [9.3 Structural Diagnostics](https://proteindesign.academy/module/9/3)
- [9.4 Energy Landscapes](https://proteindesign.academy/module/9/4)
- [9.5 Thermostability Engineering](https://proteindesign.academy/module/9/5)
- [9.integration Run a Stability Prediction](https://proteindesign.academy/module/9/integration)
- [The Stability Optimizer](https://proteindesign.academy/module/9/capstone)
- [Use the Tools](https://proteindesign.academy/module/9/tools)
- [Start Here](https://proteindesign.academy/start-here)
- [Tools & Papers](https://proteindesign.academy/tools-and-papers)
- [Continuing Practice](https://proteindesign.academy/continuing-practice)