ToxiCompass: an evidence-tracked benchmark for short-peptide toxicity screening and confidence-aware assay prioritization.

Binary peptide-toxicity predictors support early screening but do not indicate which assays should follow a toxin-like prediction. We present ToxiCompass, an evidence-tracked benchmark and two-stage protocol for short-peptide toxicity screening and assay-family prioritization. The benchmark contains 6114 peptides reconstructed from online database of biotoxins and reviewed Universal Protein Knowledgebase records, including curated toxin-positive peptides and length-matched operational comparators. Among 2866 Stage 2 candidate toxin-positive peptides, 2858 retained at least one observed-positive target/effect-family label after evidence review. Exact-sequence merging, provenance tracking, Many-against-Many sequence searching 2 clustering at 90% sequence identity (MMSeqs90) cluster-level splitting, and explicit evidence rules define the evaluation. Stage 1 assigns a toxin-like score relative to the operational-comparator population, whereas Stage 2 ranks 13 broad target/effect families to prioritize follow-up assays for toxin-positive peptides with retained evidence. On the primary MMSeqs90 cluster split, Stage 1 achieved an area under the receiver operating characteristic curve of 0.9871 and an area under the precision-recall curve of 0.9867, while Stage 2 achieved a Hit@3 of 0.8955. In a more conservative grouped-split sensitivity analysis, Stage 2 Hit@3 was 0.6506. Together, these results support ToxiCompass as a reproducible benchmark linking toxin-like peptide screening with evidence-aware prioritization of follow-up assay families.