ipsae
Installation
SKILL.md
ipSAE Binder Ranking
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.8+ | 3.10 |
| NumPy | 1.20+ | Latest |
| RAM | 8GB | 16GB |
Overview
ipSAE (interprotein Score from Aligned Errors) is a scoring function for ranking protein-protein interactions predicted by AlphaFold2, AlphaFold3, and Boltz1. It separates true from false predicted complexes more reliably than ipTM, which dilutes interface confidence across disordered or accessory regions. In a separate binder meta-analysis (Overath et al. 2025), AF3 ipSAE_min gave a 1.4-fold gain in average precision over the ipAE score that RFdiffusion pipelines commonly filter on.
Paper: Dunbrack, "Rēs ipSAE loquuntur: What's wrong with AlphaFold's ipTM score and how to fix it", bioRxiv 2025.02.10.637595