Mirror-Score: Calibrated, Inference-only Scoring Exposes the Limits of Sequence-compatibility Ranking in D-peptide Design

Jiada Li

D-peptides combine protease resistance with high target specificity, but computational design of D-peptide binders remains immature. Mirror-Peptidizer introduced an in silico mirror-image screening pipeline using target reflection, backbone generation, and ProteinMPNN sequence design, but its raw ProteinMPNN negative log-likelihood (NLL) ranking was not validated against measured affinities, and only 4 of 9 tested MDM2 designs bound detectably. We introduce Mirror-Score, a calibrated, inference-only scoring framework for heterochiral D-peptide/L-protein complexes, and a public benchmark of 31 crystal complexes across four target families, including 18 with literature-verified affinities. Raw ProteinMPNN NLL is not a valid affinity ranker: its pooled Spearman correlation with affinity is 0.19, and correlations reverse between MDM2/CHIP (+0.62) and gp41 (-0.70). We therefore evaluate Boltz-2 mirror-space cofolding confidence. For the complete viral-entry family (7 structures representing 3 peptides), interface predicted local distance difference test (pLDDT) achieves structure-level leave-one-out Spearman rho = 0.90 (p = 0.006) and correctly orders all three peptides by affinity,…