MRGPRX2-allergen docking data: D184 salt bridge analysis of 11 protein allergens using HADDOCK3

MRGPRX2 D184 engagement by food and pollen allergens: a computational hypothesis for IgE-independent mast-cell activation Docking coordinates, analysis tables, and figure-generating scripts for the manuscript "MRGPRX2 D184 engagement by food and pollen allergens: a computational hypothesis for IgE-independent mast-cell activation" (Suzuki et al., under peer review). This dataset contains HADDOCK3 protein-protein docking results for 11 clinically relevant protein allergens and 3 positive-control agonists docked against the MRGPRX2 receptor (PDB: 7VV6). Contents: (1) Strategy A docking coordinate PDB files for all clusters, (2) input ligand and receptor structures, (3) analysis tables (HADDOCK scores, D184 salt-bridge detection, inter-strategy agreement, in silico mutagenesis, negative-control docking, PRODIGY affinity, net-charge analysis), and (4) Python/PyMOL scripts for reproducing the figures. Version 2 (Revision 1, 2026): Adds the negative-control (decoy) docking experiment (ubiquitin, ribonuclease A, carbonic anhydrase II, maltose-binding protein), PRODIGY binding-affinity estimates, net-charge analysis (engagement tracks local Lys/Arg accessibility, not net charge), the unified cationic-N D184 criterion recomputation (Table S5, n=20 + pairwise kappa), and mature-chain Cry j 2 re-docking (reclassified LOW). Structure provenance corrected: Pru p 7 (PDB 8X67) and Cry j 7 (PDB 8X0R) are experimental NMR structures. Scripts included for reproduction. Version 3 (2026): Restores the raw HADDOCK3 docking coordinates and input structures (MRGPRX2_docking_coordinates_and_inputs.zip) so that the latest version is self-contained. The superseded Version 1 analysis tables and figure scripts (phase7a/phase13c/phase13e, agreement_metrics, allergen_degranulation_prediction, fig2_validation.py, fig3_heatmap.py) are intentionally omitted to avoid distributing outdated values; the corrected analyses are provided as the separate files in this record (see the archive README). Version 4 (2026): Corrects residual precursor-chain Cry j 2 values that persisted in several files from earlier versions, bringing them into agreement with the mature-chain (388-aa) values reported in the manuscript. Updated items: the size-bias correlation table and summary (molecular weight vs score Spearman ρ 0.36→0.27; electrostatic energy vs score 0.84→0.91; buried surface area vs score −0.68→−0.84; molecular weight vs BSA −0.29→−0.05), the size-bias analysis script (Cry j 2 reclassified LOW), Figure 1, Figure 2 and the supplementary size-bias figure (Cry j 2 now shown as a LOW-consistency marker), and the consistency-versus-score Spearman correlation (ρ −0.466→−0.531, correcting a tie-uncorrected computation). The superseded rho_scenarios.tsv was removed and replaced by rho_consistency_vs_score_CORRECTED.tsv. The mature-chain phase7a (top-cluster and all-cluster HADDOCK score tables) and phase13c (D184 salt-bridge consistency matrix with recomputed inter-strategy agreement), omitted from Version 3 as outdated Version 1 tables, are re-included here in corrected form. The raw HADDOCK3 docking coordinates and input structures (MRGPRX2_docking_coordinates_and_inputs.zip) are retained so this version remains self-contained. All corrected values remain statistically non-significant, and none of the results, interpretations, or conclusions changes. A file-by-file changelog is provided in CORRECTIONS_README.md.