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 B27:05, not B27:02.
<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 B27:05 below (more bound than) B27:02 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.