From Code to Fold

Interdisciplinary Protein Design

From Code to Fold

A 14-week interdisciplinary journey through protein design, combining biology, mathematics, computation, and artificial intelligence

14
Weeks
7
Disciplines
42
Coding Labs
100+
Resources

Interdisciplinary Approach

Bridge the gap between computational methods and biological understanding

Computational Methods

Python programming, molecular dynamics, and simulation techniques

Structural Biology

Protein structure, folding mechanisms, and thermodynamics

AI & Machine Learning

AlphaFold, neural networks, and generative protein design

Collaborative Learning

Group projects, peer review, and interdisciplinary discussions

14-Week Curriculum

Progressive learning from fundamental concepts to advanced applications

Week 1Foundation
Proteins as Biological Machines
  • Central Dogma
  • 20 amino acids
  • Protein folding
Week 2Mathematics
Mathematical Foundations
  • 3D geometry
  • Symmetry operations
  • Chirality
Week 3Structure
Levels of Protein Structure
  • Primary to Quaternary
  • Secondary motifs
  • Domains
Week 4Physics
Forces Shaping Proteins
  • Hydrogen bonds
  • Hydrophobic effect
  • Thermodynamics
Week 5Biology
Biosynthesis & Synthetic Biology
  • Ribosome mechanism
  • Cell-free synthesis
  • Codon table
Week 6Mathematics
Protein Geometry & Topology
  • Protein knots
  • Contact maps
  • Graph theory
Week 7Computation
Protein Modeling Basics
  • Homology modeling
  • Threading
  • Ab initio methods
Week 8Computation
Molecular Dynamics & Simulation
  • Force fields
  • MD integration
  • Folding simulations
Week 9Physics
Thermodynamics & Energy Landscapes
  • Energy funnels
  • Misfolding
  • Levinthal's paradox
Week 10AI/ML
AI & Machine Learning
  • AlphaFold
  • Neural networks
  • Generative design
Week 11Application
Enzyme Design & Catalysis
  • Transition states
  • Directed evolution
  • Active sites
Week 12Application
Proteins in Medicine & Materials
  • Antibodies
  • Vaccine design
  • Nanomaterials
Week 13Case Study
Case Studies in Protein Design
  • De novo design
  • Foldit
  • Mini-proteins
Week 14Project
Capstone Project & Presentations
  • Target selection
  • Design proposal
  • Presentations

Learning Resources

Comprehensive materials including readings, coding exercises, and visualizations

Scientific Literature

Curated papers from Nature, Science, and specialized journals

  • AlphaFold breakthrough papers
  • Protein folding reviews
  • Machine learning applications
  • Case studies in design
Coding Exercises

Hands-on Python programming with BioPython, PyMOL, and more

  • Sequence analysis scripts
  • Molecular dynamics simulations
  • Structure visualization
  • Machine learning models
Interactive Tools

Web-based tools for exploring protein structures and dynamics

  • Mol* Viewer integration
  • PDB structure browser
  • Energy landscape plots
  • Folding animations

Ready to Start Your Journey?

Join researchers and students from around the world in exploring the fascinating intersection of biology, computation, and artificial intelligence.