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ipsae

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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 than ipTM or iPAE. For structure prediction, use chai or alphafold. For QC thresholds, use protein-qc.

When to use

• Ranking binder designs for experimental testing
• Filtering BindCraft or RFdiffusion outputs
• Comparing AF2/AF3/Boltz predictions
• Predicting binding success rates
• Ranking designed binders
• Scoring AlphaFold2, AlphaFold3, or Boltz1 predictions

When not to use

• Structure prediction
• QC thresholds
• Ranking natural complexes
• Single proteins
• ESMFold predictions

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