Rapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases (ChEMBL, DGIdb), and literature surveillance (PubMed/EuropePMC). Use for emerging-pathogen profiling, antiviral candidate identification, a

COMPUTE, DON'T DESCRIBE When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it. 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; respond in user's language REASONING STRATEGY — Start Here : Start with pathogen identification: What type of organism? (virus, bacteria, fungus, parasite). Then ask: What are the essential proteins? (required for replication or viability — cannot be mutated away) Which are surface exposed? (accessible to drugs and antibodies) Which are conserved across strains? (targeting conserved regions prevents resistance escape) These three questions define your drug targets and vaccine candidates. Organisms in the same genus share targets — look up drug precedent for related pathogens before predicting from scratch. LOOK UP DON'T GUESS : Never assume a pathogen's taxonomy, genome size, or protein function. Always call BVBRC search taxonomy or UniProt search first. Even well known pathogens have strains with different drug susceptibility profiles — look up the specific strain when known. 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] for drug development" "Can we repurpose [drug] against [pathogen]?" Critical Workflow Requirements 1. Report First Approach (MANDATORY) 1. Create [PATHOGEN] outbreak intelligence.md FIRST with section headers 2. Progressively update as data is gathered 3. Output separate files: [PATHOGEN] drug candidates.csv , [PATHOGEN] target proteins.csv 2. Citation Requirements (MANDATORY) Every finding must have inline source attribution: Phase 0: Tool Verification Known Parameter Corrections Tool WRONG Parameter CORRECT Parameter NCBIDatasets get taxonomy name tax id (integer) or use BVBRC search taxonomy for keyword search UniProt search name query ChEMBL search targets query , target pref name contains (substring match) get diffdock info protein file protein (content) drugbank full search (may fail) Use drugbank vocab search as primary DrugBank lookup PubMed tip : Use sort="relevance" (default) not sort="pub date" — date sorted queries can return empty for narrow topics. Tool name: PubMed search articles . FDA labels : Use FDA get drug label info by field value with targeted return fields to avoid oversized responses from OpenFDA search drug labels . Workflow Overview Phase Summaries Phase 1: Pathogen Identification Classify via NCBI Taxonomy (query param). Identify related pathogens with existing drugs for knowledge transfer. Determine genome/proteome availability. Genome assembly availability and QC : After classifying the pathogen, use NCBIDatasets list genomes by taxon (params taxon as tax id, limit , reference only ) to find the reference genome, NCBIDatasets get genome assembly (param accession , e.g. "GCF 000005845.2") for assembly metrics (length, N50, GC%, contig/chromosome counts), and NCBIDatasets get sequence reports (param accession ) to map replicons (chromosomes/plasmids with RefSeq/GenBank accessions). For the full assembly QC to characterization workflow, see the tooluniverse microbial genome characterization skill. Open pathogen genomic surveillance : For the priority pathogens covered by Pathoplexus (west nile, ebola zaire, ebola sudan, cchf, mpox), use Pathoplexus count sequences (params organism , group by e.g. geoLocCountry or lineage) to gauge sequencing volume and geographic/lineage spread, and Pathoplexus get mutations (params organism , min proportion e.g. 0.95) to pull characteristic high prevalence mutations for the circulating population. Use early to quantify outbreak footprint and flag conserved mutations before target selection. Knowledge transfer principle : Drugs effective against related pathogens are the highest priority repurposing candidates. A protease inhibitor for SARS CoV 1 is immediately relevant to SARS CoV 2. Look up the related pathogen's approved drugs in ChEMBL before generating candidates from first principles. Phase 2: Target Identification Search UniProt for pathogen proteins (reviewed). Check ChEMBL for drug precedent. Score targets by: Essentiality (30%), Conservation (25%), Druggability (25%), Drug precedent (20%). Aim for 5+ targets. Phase 3: Structure Prediction Use NvidiaNIM AlphaFold2 for top 3 targets. Assess pLDDT confidence. Only dock structures with pLDDT 70 (active site 90 preferred). Fallback: alphafold get prediction or ESMFold predict structure. Phase 4: Drug Repurposing Screen Source candidates from: related pathogen drugs, broad spectrum antivirals, target class drugs (DGIdb). Dock top 20+ candidates via get diffdock info. Rank by docking score and evidence tier. Phase 4.5: Pathway Analysis Use KEGG to identify essential metabolic pathways. Map host pathogen interaction points. Identify pathway based drug targets beyond direct protein inhibition. Phase 5: Literature Intelligence Search PubMed (peer reviewed), BioRxiv/MedRxiv (preprints critical for outbreaks), ArXiv (computational), ClinicalTrials.gov (active trials). Track citations via OpenAlex. Note: preprints are NOT peer reviewed. Phase 6: Report Synthesis Aggregate all findings into final report. Grade every candidate. Provide 3+ immediate actions, clinical trial opportunities, and research priorities. Evidence Grading Tier Symbol Criteria Example T1 [T1] FDA approved for this pathogen Remdesivir for COVID T2 [T2] Clinical trial evidence OR approved for related pathogen Favipiravir T3 [T3] In vitro activity OR strong docking + mechanism Sofosbuvir T4 [T4] Computational prediction only Novel docking hits Completeness Checklist Phase 1: Pathogen ID [ ] Taxonomic classification complete [ ] Related pathogens identified [ ] Genome/proteome availability noted Phase 2: Targets [ ] 5+ targets identified [ ] Essentiality documented [ ] Conservation assessed [ ] Drug precedent checked Phase 3: Structures [ ] Structures predicted for top 3 targets [ ] pLDDT confidence reported [ ] Binding sites identified Phase 4: Drug Screen [ ] 20+ candidates screened [ ] FDA approved drugs prioritized [ ] Docking scores reported [ ] Top 5 candidates detailed Phase 5: Literature [ ] Recent papers summarized [ ] Active trials listed [ ] Resistance data noted Phase 6: Recommendations [ ] 3+ immediate actions [ ] Clinical trial opportunities [ ] Research priorities Fallback Chains Primary Tool Fallback 1 Fallback 2 NvidiaNIM alphafold2 (requires NVIDIA API KEY env var; free key at build.nvidia.com) alphafold get prediction (AlphaFold DB by UniProt) ESMFold predict structure get diffdock info NvidiaNIM boltz2 (requires NVIDIA API KEY env var; free key at build.nvidia.com) Manual docking NCBIDatasets suggest taxonomy UniProtTaxonomy get taxon Manual classification ChEMBL search drugs drugbank vocab search PubChem bioassays References File Contents [TOOLS REFERENCE.md](TOOLS REFERENCE.md) Complete tool documentation [phase details.md](phase details.md) Detailed code examples and procedures for each phase [report template.md](report template.md) Report template with section headers, checklist, and evidence grading [CHECKLIST.md](CHECKLIST.md) Pre delivery verification checklist (quality, citations, docking) [EXAMPLES.md](EXAMPLES.md) Full worked examples (coronavirus, CRKP, limited info scenarios)

tooluniverse-infectious-disease