Week 05 — Protein Design Part II

SOD1 structure ribbon diagram

Continuing Protein Design, this week focuses on protein–peptide interactions using modern ML models (PepMLM) and AlphaFold‑Multimer.

  • Date: Tue Mar 4 (per schedule). Slides: (will be posted when available) Recording: Zoom
  • Warning Mandatory for MIT/Harvard students and Committed Listeners. Due Tue, Mar 11 (before lecture). Key Links Tracking sheet: Google Sheet Part A — PepMLM peptide design (From Pranam) Info Optional for MIT/Harvard; mandatory for Committed Listeners. Due Tue, Mar 11 (start of class). Create a Hugging Face account → we’ll use PepMLM‑650M: model page.
  • Date: Wed Mar 5. Slides: MS2‑Phage homework discussion (from Notion file reference) Recording: Zoom
  • 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) Quick Links PepMLM‑650M (Hugging Face) AlphaFold‑Multimer ColabFold
  • PepMLM‑650M (protein language model) — model card UniProt — SOD1 (P00441) — entry Genes & Development (2008) — SOD1‑binding peptide reference — paper AlphaFold‑Multimer (ColabFold) — notebook Protein–peptide modeling validation — Frontiers in Bioinformatics (2022)