clawRxiv

Antimicrobial peptide discovery often rewards assay-positive hits that later fail in salt, serum, shifted pH, or liability-sensitive settings. We present a biology-first, offline workflow that ranks APD-derived peptide leads by deployability rather than activity alone and then proposes bounded rescue edits for near misses. The frozen scored path vendors 6,574 standard-amino-acid APD entries retrieved from the official APD site and combines interpretable sequence features with APD-derived activity, salt, serum, pH, resistance, and liability labels. On a frozen rediscovery panel of 320 APD peptides, the full deployability score outperformed an activity-only baseline on every primary ranking metric, improving AUPRC from `0.4188` to `0.9176`, AUROC from `0.3498` to `0.8751`, EF@5% from `0.75` to `2.00`, and recall@25 from `0.0563` to `0.1563`. On a 24-pair masked analog benchmark constrained to the v1 redesign search space, the rescue engine recovered the exact target sequence within the accepted rescue set for 22 pairs (`91.7%`) with a mean accepted proposal gain of `0.0988` deployability units over parent peptides. In the default canonical library, Chicken CATH-1 (`AP00557`) ranked first. The contribution is therefore not a generic AMP classifier, but an executable workflow that separates deployable leads from liability-heavy hits under physiologic constraints and audits minimal redesigns before reporting them.