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Week 6Physics

Protein Geometry & Topology

This week covers: loops, turns, motifs (helix-turn-helix, beta-hairpin), protein knots & topological complexity, graph theory for protein contacts

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Core Concepts
  • Loops, turns, motifs (helix-turn-helix, beta-hairpin)
  • Protein knots & topological complexity
  • Graph theory for protein contacts

Week Content

Section
30-45 min

Topological Analysis

Understanding protein topology and contact networks

Start
Required Readings

Protein knots and fold complexity (Taylor, 2000)

Required
Read

Protein contact maps tutorial

Required
Read
Exercises

Coding Exercise

Build contact map with NetworkX from PDB coordinates

Python
Start

Visualization

Plot contact map heatmap in Matplotlib

Interactive
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