Lab — Protein Design Part II

Tip

This week’s practical work is in‑silico and pairs with the Homework: design peptides with PepMLM and evaluate binding to SOD1 using AlphaFold‑Multimer.

Objective

Model protein–peptide interactions by generating peptide candidates (PepMLM‑650M) and predicting complexes (AlphaFold‑Multimer). Compare ipTM scores across candidates to select promising binders.

Concepts You’ll Learn

  • Protein language models for peptide design
  • Multimeric structure prediction (protein–peptide)
  • ipTM as a binding‑confidence heuristic
  • Practical workflows in Google Colab (GPU)

SOD1 ribbon structure