Protocol-aware partner ranking — diagnostic evaluation resource (v1.0)

Diagnostic evaluation resource for the Briefings in Bioinformatics Problem Solving Protocol: Protocol-aware benchmarking of constrained biological partner ranking: a case study in virus–host PPI. This Zenodo deposit holds large binary artefacts that exceed GitHub's file-size limit: retrieval_gnn_tau007_longrun_best_model.pt (~5.3 GB) — retrieval diagnostic checkpoint classification_esm3_frozen_best_model.pt (~5.3 GB) — classification diagnostic checkpoint train_protein_pairs.pkl (~386 MB) — HVIDB training pairs Code, embed caches, evaluation JSON/NPZ, and scripts: https://github.com/Xindi-Wang1004/protocol-aware-partner-ranking-eval Release tag: v1.0-diagnostic-eval Not included: ESM3 base weights (download separately under EvolutionaryScale / Hayes et al. 2025 license). Upstream sources: HVIDB (doi:10.1093/bib/bbaa425); IntAct (doi:10.1093/nar/gkt1115).