ML Protein Design Bootcamp 2025

Self-paced course

Build judgment across modern ML protein design workflows.

This bootcamp moves from environment setup to structure prediction, backbone generation, docking, and a binder-design capstone. Each section is meant to produce something concrete: a configured tool, a prediction, a comparison, or a design decision.

Start with Monday Preview capstone
Capstone workflow from target selection through validation and final design selection.

Your progress

Course checkpoint tracker

Completion is saved in this browser. Use it to keep track of setup and verification steps as you move through the course.

0 completed checkpoints
0%

Course Dashboard

HPC setup path showing login node, scheduler, GPU node, and verification commands. MondayPre-work + 13 modules Tool Installation Set up HPC access, CUDA, conda environments, containers, and the core prediction and design tools. Required foundationOpen Monday -> Structure prediction confidence dashboard with a pLDDT profile and PAE heatmap. Tuesday4 modules Structure Prediction Use PyMOL, AlphaFold2, and ESMFold to predict structures and interpret confidence instead of treating outputs as answers. Analysis heavyOpen Tuesday -> RFdiffusion output gallery showing unconditional, motif, hotspot, and symmetric backbone designs. Wednesday2 modules Advanced Prediction and Design Compare complex prediction tools, then generate and inspect protein backbones with RFdiffusion workflows. Design workflowOpen Wednesday -> CPU versus GPU timing chart showing vectorization and workload-size effects. Thursday4 modules Compute, Docking, and Reflection Connect PyTorch basics to GPU performance, docking intuition, and planning decisions for the capstone. Compute intuitionOpen Thursday -> Binder design target interface showing a target chain, hotspot residues, and a designed binder. CapstoneCurated target set Protein Binder Design Project Choose a target, define a binding face, generate binders, design sequences, validate structures, and document the rationale behind your choices. ProjectOpen Capstone ->

Getting Started

  1. Start with the Monday HPC setup if you have not confirmed GPU access and environment paths.
  2. Move through the days in order when possible; later activities assume earlier tools and concepts.
  3. Use the checkboxes on setup pages only after the command, output, or file exists.
  4. Return anytime and use the resume banner to pick up where you left off.

Report an Issue / Ask a Question (GitHub account required)