# Module 5: The Explorer

> Explore how proteins bind ligands, catalyze reactions, and recognize partners.

Function & Molecular Recognition

Explore how proteins bind ligands, catalyze reactions, and recognize partners.

- Identify what proteins bind, and the chemical features that make a molecule bindable
- Locate pockets on a molecular surface and judge which of them are druggable
- Read electrostatic surfaces and apply charge complementarity to a binding problem
- Assess shape complementarity and buried surface area at an interface
- Explain how a catalytic triad works and why its geometry has so little tolerance
- Design a binding site by carving a pocket and lining it with complementary residues

## Links

- [Introduction](https://proteindesign.academy/module/5/intro)
- [5.1 Molecules 101: What Proteins Bind](https://proteindesign.academy/module/5/1)
- [5.2 Surface Topography and Pocket Detection](https://proteindesign.academy/module/5/2)
- [5.3 Electrostatic Surfaces](https://proteindesign.academy/module/5/3)
- [5.4 Shape Complementarity](https://proteindesign.academy/module/5/4)
- [5.5 Enzyme Catalysis: The Catalytic Triad](https://proteindesign.academy/module/5/5)
- [5.integration Design a Binding Site](https://proteindesign.academy/module/5/integration)
- [Target Acquisition](https://proteindesign.academy/module/5/capstone)
- [Use the Tools](https://proteindesign.academy/module/5/tools)
- [Start Here](https://proteindesign.academy/start-here)
- [Tools & Papers](https://proteindesign.academy/tools-and-papers)
- [Continuing Practice](https://proteindesign.academy/continuing-practice)