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README.md

@@ -28,6 +28,31 @@ Code: https://github.com/GainGod-Xu/OccupancyFlow
 | `weights/interactome_weights_0630.xlsx` | 328,378 | the weight file used by the disease-module analyses |
 | `negatome_check/predictions_negatome_random.csv` | 6,352 | predictions for Negatome human non-interactions, Negatome pairs that are also reported interactions, and random pairs of the same proteins |
 | `negatome_check/per_protein_comparison.csv` | 283 | per-protein median ΔG for reported partners vs Negatome partners |
+| `fixed_test_sets/test_s79_fixed.csv` | 111 | S79 with the 1E96 label restored — all 111 chain pairs labelled |
+| `fixed_test_sets/test_s90_fixed.csv` | 90 | S90 with 3H6G added (chains A–B) — all 90 complexes |
+| `official_supplementary/` | — | the upstream sources as published: PPI-Affinity SI files 3 and 4 (labels), the ProAffinity chain list, the PPAP pdbbind90 chain list |
+
+## Defects in the benchmark sources, and what was fixed
+
+Audited against the published supplementary files; the full write-up is in
+[docs/data_provenance.md](https://github.com/GainGod-Xu/OccupancyFlow/blob/main/docs/data_provenance.md).
+
+- **S79 loses one complex in the official file.** PDB code `1E96` is stored as `1.00E+96` — Excel
+  read it as scientific notation before publication. Any pipeline joining on the PDB name drops it,
+  so published S79 numbers are most likely computed on 78 of 79 complexes. The label survives
+  (7.4 kcal/mol) and is confirmed by the ProAffinity pKd for the same entry (5.5686 → 7.60).
+  `fixed_test_sets/test_s79_fixed.csv` restores it.
+- **S90 loses one complex to the chain list.** The labels cover 90 complexes; the PPAP chain list
+  covers 89. The missing entry, 3H6G, has an unambiguous interface (chains A–B, 355 heavy-atom
+  contacts within 4.5 Å, minimum distance 2.75 Å) and is a homodimer, which may be why it was
+  excluded. `fixed_test_sets/test_s90_fixed.csv` adds it back.
+- **The two official files use opposite sign conventions**: SI-File-3 stores |ΔG| (positive,
+  4.3–18.6), SI-File-4 stores ΔG (negative, −18.1 to −3.3). Files here are all ΔG (negative).
+- **Label quality is good**: cross-checking S79 against the independent ProAffinity pKd values
+  gives a median absolute difference of 0.032 kcal/mol over the 78 shared complexes.
+
+Keep the original `affinity/test_s79.csv` and `test_s90.csv` when comparing against published
+numbers, which were computed on the uncorrected sets.
 
 ## Things to know before using these files