| --- |
| license: cc-by-nc-4.0 |
| task_categories: |
| - tabular-regression |
| tags: |
| - protein-protein-interaction |
| - binding-affinity |
| - interactome |
| --- |
| |
| # 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](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 |
|
|
| - **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`. |
|
|
