ML Protein Design Bootcamp 2025
Welcome to the ML Protein Design Bootcamp 2025! This self-paced course covers machine learning tools for protein structure prediction and design.
Course Overview
This bootcamp is organized into 4 days of content plus a capstone project. Each day contains sequential modules that build on each other.
Monday
Tool Installation: Install essential ML protein design tools on your HPC cluster including LocalColabFold, ESMFold, LigandMPNN, RFdiffusion2, Chai-1, Boltz-2, and BindCraft.
Tuesday
Structure Prediction: Learn protein visualization with PyMOL, predict structures with AlphaFold2, and compare prediction methods (ESMFold vs AF2) to understand their trade-offs.
Wednesday
Advanced Prediction & Design: Compare AlphaFold3 and Chai-1 on complex predictions, then design proteins with RFdiffusion including binders and symmetric oligomers.
Thursday
Docking & Reflection: Explore CPU vs GPU computing with a hands-on PyTorch activity, learn molecular docking for protein-ligand interactions, and reflect on your learning before starting the capstone project.
Protein Binder Capstone Project
De Novo Binder Design: Design a protein binder for a target of your choice using RFdiffusion, LigandMPNN, and structure prediction tools. Choose from therapeutic targets like PD-L1, enzymes like TEM-1 beta-lactamase, or allergens like Bet v 1.
Your Progress
Completed modules: 0
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Getting Started
- Choose a day from the navigation above or the cards below
- Work through modules in order - each builds on the previous
- Check off sections as you complete them - your progress is saved automatically
- Return anytime - use the “Resume” button to pick up where you left off