tooluniverse-infectious-disease
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-infectious-disease --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Rapid response system for emerging pathogens using taxonomy analysis, target identification, structure prediction, and computational drug repurposing.
How it works
- Proceeds through a phased workflow: Pathogen Identification (taxonomy, relatives, genome/proteome availability) to Phase 1 output a pathogen profile; Phase 2 identifies essential, druggable targets and ranks them by criteria (essentiality, conservation, druggability, drug precedent) to produce a prioritized target list; Phase 3 predicts 3D structures (AlphaFold2 via NvidiaNIM) and assesses quality with pLDDT, identifying docking-ready targets and binding sites; Phase 4 screens repurposing candidates from related pathogens, broad-spectrum antivirals, and target-class drugs, and runs docking with NvidiaNIM_diffdock to rank candidates; Phase 4.5 analyzes KEGG pathways and host-pathogen interactions for additional drug targets; Phase 5 gathers literature intelligence from PubMed, BioRxiv, MedRxiv, ArXiv, and clinical trials; Phase 6 synthesizes a final report with top candidates and recommended actions.
When to use it
Apply when user asks about new pathogens, emerging pathogens, drug repurposing candidates, or essential drug targets for drug development.
What it can touch
- Tools referenced include: NCBI_Taxonomy_search, UniProt_search, ChEMBL_search_targets, NvidiaNIM_alphafold2, NvidiaNIM_diffdock, PubMed_search_articles, BioRxiv_search_preprints, MedRxiv_search_preprints, ArXiv_search_papers, Clinial trials search utilities. (All tool calls and parameters must align to the exact names and usage shown in the skill.)
Caveats
- The workflow emphasizes speed and actionable output with evidence grading; outputs include multiple file types such as reports and CSVs as part of mandatory outputs. Specific licensing or risk notes are not provided in the excerpt.
# Infectious Disease Outbreak Intelligence Rapid response system for emerging pathogens using taxonomy analysis, target identification, structure prediction, and computational drug repurposing. **KEY PRINCIPLES**: 1. **Speed is critical** - Optimize for rapid actionable intelligence 2. **Target essential proteins** - Focus on conserved, essential viral/bacterial proteins 3. **Leverage existing drugs** - Prioritize FDA-approved compounds for repurposing 4. **Structure-guided** - Use NvidiaNIM for rapid structure prediction and docking 5. **Evidence-graded** - Grade repurposing candidates by evidence strength 6. **Actionable output** - Prioritized drug candidates with rationale 7. **English-first queries** - Always use English terms in tool calls (pathogen names, protein names, drug names), even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language --- ## When to Use Apply when user asks: - "New pathogen detected - what drugs might work?" - "Emerging virus [X] - therapeutic options?" - "Drug repurposing candidates for [pathogen]" - "What do we know about [novel coronavirus/bacteria]?" - "Essential targets in [pathogen]
- When to Use
- Critical Workflow Requirements
- 1. Report-First Approach (MANDATORY)
- 2. Citation Requirements (MANDATORY)
- Phase 0: Tool Verification
- Known Parameter Corrections
- Workflow Overview
- Phase 1: Pathogen Identification
- 1.1 Taxonomic Classification
- 1.2 Related Pathogens (Knowledge Transfer)
- 1.3 Output for Report
- Phase 2: Target Identification
- 2.1 Essential Protein Identification
- 2.2 Target Prioritization Criteria
What does the tooluniverse-infectious-disease skill do?
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging infections, or needing rapid therapeutic options during outbreaks.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-infectious-disease --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.