Xu-AI4Science/occupancyflow-data

OccupancyFlow data

Data for the OccupancyFlow pipeline: sequence-based binding-affinity prediction and the competition-adjusted weighting of the human interactome. Code: https://github.com/GainGod-Xu/OccupancyFlow

Contents

path	rows	what it is
affinity/train_6655_no_overlap_s79_s90.csv	6,655	chain pairs with a measured Kd, converted to ΔG (kcal/mol). Curated from PPB-Affinity: chain-pair decomposition, interface filtering, deduplication, then removal of every PDB entry shared with S79/S90
affinity/test_s79.csv	111	S79 benchmark (110 labelled), sequences re-extracted per chain from RCSB
affinity/test_s90.csv	89	S90 benchmark
interactome/edges_RSW_20231018_filtered.csv	328,433	human interaction network (Entrez gene IDs + symbols) after removing proteins without a reference sequence
interactome/proteins_RSW_20231018_clean.csv	17,219	protein table: sequence, PaxDb abundance (ppm), identifiers
interactome/predictions_esmc_300M_nM.csv	328,433	predicted ΔG and Kd per interaction (esmc_300M, current), plus abundances
weights/interactome_weights_esmc_300M.csv	328,422	competition-adjusted weights w_ij, complex and free concentrations - current selected encoder (esmc_300M); the weight file the manuscript and disease-module analyses use
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.

• 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

• ΔG sign convention: negative means binding. Kd in nM.
• Affinity values in the interactome files are predictions, not measurements, and they are compressed: SD 0.64 kcal/mol against 2.68 for the measured training labels. They order interactions better than they calibrate them.
• The predictions do not distinguish interactions from non-interactions (Negatome AUC 0.481); the model was trained only on binders. See negatome_check/.
• Abundance conversion uses k = 1.881 nM/ppm (hepatocyte GAPDH: 3.39e7 copies/cell, 3,000 fL, divided by the PaxDb whole-organism abundance 9,978 ppm).
• 44 titin (TTN) interactions are missing from the weighted network: the 34,350-residue sequence broke an intermediate spreadsheet export. They are present in the interactome/edges file and absent downstream.
• Leakage control in the affinity split is at PDB-entry level, not sequence identity: 2 of 111 S79 chain pairs have both sequences present in the training set (S90: none).

Sources

PPB-Affinity (Liu et al., Sci Data 2024) · PPI-Affinity S79/S90 (Romero-Molina et al., JPR 2022) · PaxDb (Wang et al. 2015) · Negatome 2.0 (Blohm et al., NAR 2014) via Synthyra/NEGATOME.