NefroStat/HLA-Structural-Immunogenicity: Manuscript Submission Version

Major Methodological Update: The Dual-Filter Framework This major release upgrades the histocompatibility assessment pipeline from a purely structural model to a comprehensive dual-filter structural and biophysical framework. Key Implementations: Biophysical Reactivity Filter: Added empirical 5th percentile thresholds for electrostatic charge and hydrophobicity. Mismatches are now filtered not only by steric accessibility but also by their thermodynamic viability, derived exclusively from antibody-verified eplets. Updated Python Core (src/03_calc_physics.py): The eplet evaluation logic now enforces the two sequential constraints (SASA > 10 Ų AND biophysical metrics > 5th percentile). Enhanced Statistical Scripts (analysis/05_stats_and_plots.R): Updated the R analysis pipeline to reflect the dual-filter data. Includes refined Weighted Cohen's Kappa calculations and updated correlation analyses (Spearman's rank) demonstrating the partial decoupling of charge and hydrophobicity at the HLA-DP locus. Updated Documentation: Fully revised README.md reflecting the new methodology and execution steps. Note for researchers: This version corresponds to the updated manuscript submitted for peer review.