AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
K-Dense-AI/claude-scientific-skillsView
Data & Repro
IP
ipsae
Maintainer FreedomIntelligence · Last updated April 1, 2026
ipSAE (interprotein Score from Aligned Errors) is a scoring function for ranking protein-protein interactions predicted by AlphaFold2, AlphaFold3, and Bolt.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/ipsae
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- ipSAE (interprotein Score from Aligned Errors) is a scoring function for ranking protein-protein interactions predicted by AlphaFold2, AlphaFold3, and Boltz1. It outperforms ipTM and iPAE for binder design ranking with 1.4x higher precision in identifying true binders.
- Paper: What's wrong with AlphaFold's ipTM score.
Source Doc
Excerpt From SKILL.md
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):
Residue-level scores (_residues.csv):
Successful run
What good output looks like:
- ipSAE_min > 0.61 (primary filter)
- pDockQ > 0.5 (supporting metric)
- Reasonable number of interface contacts (20-100)
Use cases
- Use ipsae in research workflows aligned with this subject area.
- Follow the upstream documentation for the full working procedure.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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