# AS — ankylosing spondylitis allele case (MHC-ranking benchmark)

Three disease TCR:peptide complexes (PDB **7n2o, 7n2q, 8cx4**), FoldX-repaired on the risk allele
**HLA-B*27:05** and the closely related protective allele **HLA-B*27:02**. The recognition task is the
MHC dimension: rank alleles for a fixed TCR:peptide; the peptide is recognised on B*27:05, not B*27:02.

- `<name>.pdb`   = B*27:05 (recognised)
- `<name>_2.pdb` = B*27:02 (not recognised)
- `total_energy_summary.csv` — precomputed TCRen / MJ(HLA-pep) / MJ(TCR-HLA) / Total_score /
  pyrosetta_score for the 6 AS structures + 8 decoys (non20/non33 × yeih/prpf3).

TCRen2 result: the combined score orders B*27:05 below (more bound than) B*27:02 on all 3 pairs (3/3),
matching PyRosetta; single-interface terms fail (0/3). Source: aldan3 `/projects/structures/md/<name>/`
+ `article_plots_scripts/AS_structures_plots`.