Module 7: The Sequence Finder

Inverse Folding

Learn how ProteinMPNN designs sequences for a target structure — and how to judge the sequences it returns.

• Explain the inverse folding problem and why sequence space for a fold is astronomically large
• Apply the degeneracy principle: structure constrains core positions far more tightly than surface ones
• Redesign a surface for solubility without disturbing the core
• Run ProteinMPNN in principle: what its parameters control and what its score does and does not mean
• Rank candidate sequences on several metrics at once, knowing the best MPNN score is not always the best protein