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KosinskiLab
AlphaJudge
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30 alphajudge pae handling for af3x outputs cross linker tokens
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Sep 28, 2026
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30 alphajudge pae handling for af3x outputs cross linker tokens
#33
DimaMolod
merged 17 commits into
main
KosinskiLab/AlphaJudge:main
from
30-alphajudge-pae-handling-for-af3x-outputs-cross-linker-tokens
KosinskiLab/AlphaJudge:30-alphajudge-pae-handling-for-af3x-outputs-cross-linker-tokens
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Commits on Sep 25, 2026
Align AF3 PAE to scored residues by token identity
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Look up AF3 pair ipTM by the summary's chain order
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Keep AF3 global confidences over excluded tokens out of the metascore
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Add a real AF3x crosslink prediction as a regression fixture
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Map AF3 per-atom modified residues to their centre-atom token
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Map AF3 residues to tokens once for all token matrices
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Look up pair ipTM in Confidence rather than in Interface
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Name the confidence-scope values once
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Commits on Sep 26, 2026
Simplify scoring, report and biophysics code without changing outputs
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Compute solvation SAS for every atom of residues at the interface
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Align Boltz-2 PAE, pLDDT and pair ipTM to residues by token and chain
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Fix report PAE lookup, feature count, median and appendix numbering
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Key the ProSurf interface cache on the atoms it reads
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Harden AF3 model ranking and structure lookup
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Commits on Sep 28, 2026
Merge pull request #31 from KosinskiLab/30-simplify
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Merge pull request #32 from KosinskiLab/30-fixes
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Demote non-finite AF3 ranking scores
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