Core Topics

• Central Dogma
• 20 amino acids
• Protein folding

Required Readings

• • Alberts Ch. 3
• • Branden & Tooze Ch. 1

Coding Exercise

Amino acid properties analysis

Visualization

Protein structure gallery

Core Topics

• 3D geometry
• Symmetry operations
• Chirality

Required Readings

• • Lesk Ch. 2
• • Creighton Ch. 4

Coding Exercise

3D coordinate transformations

Visualization

Symmetry operations in proteins

Core Topics

• Primary to Quaternary
• Secondary motifs
• Domains

Required Readings

• • Richardson (1981)
• • Chothia & Lesk (1986)

Coding Exercise

Secondary structure prediction

Visualization

Ramachandran plots

Core Topics

• Hydrogen bonds
• Hydrophobic effect
• Thermodynamics

Required Readings

• • Dill (1990)
• • Kauzmann (1959)

Coding Exercise

Energy calculations

Visualization

Force field visualization

Core Topics

• Ribosome mechanism
• Cell-free synthesis
• Codon table

Required Readings

• • Ramakrishnan (2002)
• • Church et al. (2014)

Coding Exercise

Codon optimization

Visualization

Translation machinery

Core Topics

• Protein knots
• Contact maps
• Graph theory

Required Readings

• • Taylor (2000)
• • Vendruscolo et al. (2002)

Coding Exercise

Contact map analysis

Visualization

Protein topology browser

Core Topics

• Homology modeling
• Threading
• Ab initio methods

Required Readings

• • Marti-Renom et al. (2000)
• • Baker & Sali (2001)

Coding Exercise

MODELLER tutorial

Visualization

Model quality assessment

Core Topics

• Force fields
• MD integration
• Folding simulations

Required Readings

• • Karplus & McCammon (2002)
• • Shaw et al. (2010)

Coding Exercise

GROMACS simulation

Visualization

Trajectory analysis

Core Topics

• Energy funnels
• Misfolding
• Levinthal's paradox

Required Readings

• • Dill & Chan (1997)
• • Onuchic et al. (1997)

Coding Exercise

Energy landscape plotting

Visualization

Folding funnel models

Core Topics

• AlphaFold
• Neural networks
• Generative design

Required Readings

• • Jumper et al. (2021)
• • Senior et al. (2020)

Coding Exercise

Structure prediction with ColabFold

Visualization

Confidence score analysis

Core Topics

• Transition states
• Directed evolution
• Active sites

Required Readings

• • Arnold (2018)
• • Röthlisberger et al. (2008)

Coding Exercise

Active site analysis

Visualization

Catalytic mechanism viewer

Core Topics

• Antibodies
• Vaccine design
• Nanomaterials

Required Readings

• • Burton (2002)
• • King et al. (2014)

Coding Exercise

Antibody modeling

Visualization

Protein nanostructures

Core Topics

• De novo design
• Foldit
• Mini-proteins

Required Readings

• • Huang et al. (2016)
• • Cooper et al. (2010)

Coding Exercise

Design analysis pipeline

Visualization

Success story gallery

Core Topics

• Target selection
• Design proposal
• Presentations

Required Readings

• • Student-selected papers

Coding Exercise

Project implementation

Visualization

Presentation materials