Course Exercises

Hands-on coding and visualization exercises for each week of the protein design course

14 Coding Exercises14 Visualizations

codingBeginner

Week 1 Coding Exercise

Proteins as Biological Machines

Python script to compute amino acid frequencies from FASTA

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationBeginner

Week 1 Visualization

Proteins as Biological Machines

Explore insulin (PDB: 4INS) with Mol* Viewer

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingBeginner

Week 2 Coding Exercise

Mathematical Foundations: Geometry & Symmetry

NumPy script to rotate 3D helix points

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

Start View

visualizationBeginner

Week 2 Visualization

Mathematical Foundations: Geometry & Symmetry

Plot a right-handed vs left-handed helix in Matplotlib

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

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codingBeginner

Week 3 Coding Exercise

Levels of Protein Structure

Biopython script to parse PDB and count helices/sheets

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationBeginner

Week 3 Visualization

Levels of Protein Structure

Compare myoglobin vs hemoglobin structures

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingBeginner

Week 4 Coding Exercise

Forces Shaping Proteins

Compute Kyte–Doolittle hydrophobicity index for a sequence

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationBeginner

Week 4 Visualization

Forces Shaping Proteins

Color-map hydrophobic vs hydrophilic residues in PyMOL

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

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codingIntermediate

Week 5 Coding Exercise

Biosynthesis in Nature & Synthetic Biology

Translate DNA sequence to protein in Python

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationIntermediate

Week 5 Visualization

Biosynthesis in Nature & Synthetic Biology

Watch HHMI BioInteractive ribosome video

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingIntermediate

Week 6 Coding Exercise

Protein Geometry & Topology

Build contact map with NetworkX from PDB coordinates

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

Start View

visualizationIntermediate

Week 6 Visualization

Protein Geometry & Topology

Plot contact map heatmap in Matplotlib

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingIntermediate

Week 7 Coding Exercise

Protein Modeling Basics

Query UniProt API to fetch protein sequences

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationIntermediate

Week 7 Visualization

Protein Modeling Basics

Compare modeled vs natural structure with Mol*

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

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codingIntermediate

Week 8 Coding Exercise

Molecular Dynamics & Simulation

Run toy MD of alanine dipeptide with OpenMM

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationIntermediate

Week 8 Visualization

Molecular Dynamics & Simulation

Animate folding with NGLView (Jupyter)

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingIntermediate

Week 9 Coding Exercise

Thermodynamics & Energy Landscapes

Simulate toy energy landscape (2D potential surface)

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationIntermediate

Week 9 Visualization

Thermodynamics & Energy Landscapes

Plot funnel energy diagram in Matplotlib

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

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codingIntermediate

Week 10 Coding Exercise

AI & Machine Learning in Protein Design

Train simple RNN to generate amino acid strings

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

Start View

visualizationIntermediate

Week 10 Visualization

AI & Machine Learning in Protein Design

Plot sequence logos with Logomaker

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingAdvanced

Week 11 Coding Exercise

Enzyme Design & Catalysis

Locate catalytic residues using PyRosetta API

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

Start View

visualizationAdvanced

Week 11 Visualization

Enzyme Design & Catalysis

Highlight active site residues in PyMOL

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingAdvanced

Week 12 Coding Exercise

Proteins in Medicine & Materials

Simple docking simulation using PyRosetta

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

Start View

visualizationAdvanced

Week 12 Visualization

Proteins in Medicine & Materials

Docking poses in PyMOL

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

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codingAdvanced

Week 13 Coding Exercise

Case Studies in Protein Design

Download a de novo design from PDB

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationAdvanced

Week 13 Visualization

Case Studies in Protein Design

Compare designed vs natural fold families

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View

codingAdvanced

Week 14 Coding Exercise

Capstone Project & Presentations

Final project implementation

Duration:45-60 min

Language:Python

Tools:

BioPythonNumPyMatplotlib

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visualizationAdvanced

Week 14 Visualization

Capstone Project & Presentations

Group design gallery of protein structures, energy landscapes, and project notebooks

Duration:30-45 min

Language:Interactive

Tools:

Mol*PyMOLMatplotlib

Start View