The Protein-Protein Interactions Wall

Learn how to evaluate protein-protein interactions with AlphaFold3 using both pairwise and pooled strategies.

What You'll Learn

• How to run pairwise AF3 PPI baselines
• How pooled AF3 introduces decoy competition and reduces spurious hits
• How to interpret ipTM as an interface-confidence signal
• Why size correction matters for fair score comparison
• How to evaluate performance under noisy biological data

Why This Wall Matters

In real PPI discovery, signals are imperfect and false positives are common. This wall trains you to compare modeling strategies, quantify performance, and interpret uncertainty instead of over-claiming results.