Structure pAE Score

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Structure Prediction · 7 tools

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evo-design/proto-language/proto_language/constraint/protein_structure/structure_confidence_constraint.py

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Constraint contributorsdguo8412bviggiano

Evaluate structure quality using predicted aligned error (pAE).

1. Computes the average of the entire pairwise pAE matrix.
2. Normalizes by 31.75 Angstroms (the AlphaFold maximum value used by all major structure predictors).
3. Returns that value without flipping the sign, as lower is better.

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API Reference

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Usage

>>> from proto_language.core import Segment
>>> target = Segment(length=200, sequence_type="protein")
>>> binder = Segment(length=80, sequence_type="protein")
>>> af3_pae = Constraint(
...     inputs=[target, binder],
...     function=structure_pae_constraint,
...     function_config={
...         "structure_tool": "alphafold3",
...         "alphafold3_config": {"seeds": [0, 1], "use_msa": True},
...     },
... )

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