AMPHunter Overview
AMPHunter is an automated pipeline for discovering novel antimicrobial peptide (AMP) candidates from metagenomic sequences, focusing on extreme environments.
Why AMPs?
Antimicrobial resistance (AMR) is one of the most serious global health threats. The WHO estimates AMR-associated deaths could reach 10 million per year by 2050. Antimicrobial peptides — short, naturally occurring molecules produced by organisms as part of their innate immune defense — represent a promising alternative to conventional antibiotics.
Why Extreme Environments?
Organisms in extreme environments (hot springs, permafrost, deep-sea vents, glaciers) face unique selective pressures. Their defense molecules have evolved in conditions unlike anything in conventional databases — making them a rich source of truly novel sequences.
Pipeline Architecture
Metagenomic Reads (SRA/ENA)
→ Pyrodigal: smORF extraction (10-50 aa)
→ ESM-2 (650M): AMP probability scoring
→ Biophysical filter: charge, hydrophobicity, length
→ Safety Stack: hemolysis (HemoPi3), toxicity (ToxinPred3)
→ Novelty: BLAST vs DRAMP + APD3 + AMPSphere
→ Structure: ESMFold / ColabFold (top candidates)
→ Tiering: Tier-1 (leads) / Tier-2 (exploratory) / Hold / Reject
Current Status
| Biome | Status | Candidates |
|---|---|---|
| 🌋 Hot Springs | ✅ Complete | 2,001 |
| 🧊 Permafrost | ✅ Complete | 532 |
| 🏔️ Glacier | 🔄 Running | — |
| 🌊 Abyssal Ocean | 🔄 Running | — |
| 🌊 Deep-Sea Vents | ⏳ Queued | — |
All results are computational predictions. No candidate has been experimentally validated. We share results transparently for the research community.
Quick Links
- Code: github.com/Nearik42/esm2-amp
- Parent project: Prometheus
- Results: /results