ipsae
Binder design ranking using ipSAE (interprotein Score from Aligned Errors). Use this skill when: (1) Ranking binder designs for experimental testing, (2) Filtering BindCraft or RFdiffusion outputs, (3) Comparing AF2/AF3/Boltz predictions, (4) Predicting binding success rates, (5) Need better ranking
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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
How to run
Installation
git clone https://github.com/DunbrackLab/IPSAE.git
cd IPSAE
pip install numpy
AlphaFold2
python ipsae.py scores_rank_001.json unrelaxed_rank_001.pdb 15 15
AlphaFold3
python ipsae.py fold_model_full_data_0.json fold_model_0.cif 10 10
Boltz1
python ipsae.py pae_model_0.npz model_0.cif 10 10
Key parameters
| Parameter | Description | Recommended |
|---|---|---|
| PAE file | JSON (AF2/AF3) or NPZ (Boltz) | Match predictor |
| Structure file | PDB or CIF structure | Match PAE |
| PAE cutoff | Threshold for contacts | 10-15 |
| Distance cutoff | Max CA-CA distance (A) | 10-15 |
Output format
Two output files are generated:
Chain-pair scores (_chains.csv):
chain_A,chain_B,ipSAE_min,pDockQ,pDockQ2,LIS,n_contacts,interface_dist
A,B,0.72,0.65,0.58,0.45,42,8.5
Residue-level scores (_residues.csv):
chain,resnum,pSAE,pLDDT
A,45,0.85,92.3
A,67,0.78,88.1
Sample output
Successful run
$ python ipsae.py scores_rank_001.json design_0.pdb 10 10
Processing design_0...
Found 2 chains: A, B
Computing ipSAE scores...
Results written to:
design_0_chains.csv
design_0_residues.csv
Summary:
ipSAE_min: 0.72
pDockQ: 0.65
LIS: 0.45
Interface contacts: 42
What good output looks like:
- ipSAE_min > 0.61 (primary filter)
- pDockQ > 0.5 (supporting metric)
- Reasonable number of interface contacts (20-100)