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Infectious Disease Outbreak Intelligence Checklist

Pre-delivery verification checklist for outbreak intelligence reports.

Report Quality Checklist

Structure & Format

  • Report file created: [PATHOGEN]_outbreak_intelligence.md
  • All 8 main sections present
  • Executive summary completed (not [Analyzing...])
  • Data sources section populated

Phase 1: Pathogen Identification

  • Scientific name documented
  • Taxonomy ID (NCBI) provided
  • Pathogen type classified (virus/bacteria/fungus/parasite)
  • Family and genus identified
  • Full taxonomic lineage shown
  • Related pathogens with drug precedent identified
  • Genome/proteome reference noted

Phase 2: Target Identification

  • ≥5 druggable targets identified
  • Each target has UniProt accession
  • Protein function described
  • Essentiality justified
  • Conservation across strains noted
  • Drug precedent checked (related pathogens)
  • Targets ranked by druggability score
  • Top 3 targets have detailed profiles

Phase 3: Structure Prediction

  • NVIDIA_API_KEY availability documented
  • Structures predicted for top 3 targets (minimum)
  • Method stated (AlphaFold2/ESMFold)
  • Mean pLDDT reported for each structure
  • pLDDT distribution by region included
  • Binding site regions identified
  • Active site residue confidence documented
  • Docking suitability assessed

Phase 4: Drug Repurposing Screen

  • ≥20 candidate drugs identified
  • Sources documented (related pathogen, broad-spectrum, target class)
  • FDA approval status for each drug
  • Docking performed for top candidates
  • Docking scores reported with confidence
  • Top 5-10 candidates ranked
  • Mechanism of action described
  • Clinical evidence level assigned

Phase 5: Literature Intelligence

  • Recent publications searched (<6 months)
  • Key findings summarized
  • Active clinical trials listed
  • Resistance data noted (if available)
  • Previous treatment outcomes summarized

Phase 6: Recommendations

  • ≥3 immediate actions listed
  • Clinical trial opportunities identified
  • Research priorities outlined
  • Timeframe/urgency noted

Citation Requirements

Every Section Must Include

  • Source database name
  • Tool used (in backticks)
  • Specific identifiers (UniProt, NCBI, NCT, etc.)

Format Examples

*Source: NCBI Taxonomy via `NCBI_Taxonomy_search` (TaxID: 2697049)*
*Source: UniProt via `UniProt_search` (P0DTD1)*
*Source: NVIDIA NIM via `NvidiaNIM_alphafold2` (pLDDT: 91.2)*
*Source: NVIDIA NIM via `NvidiaNIM_diffdock` (score: 0.92)*
*Source: ChEMBL via `ChEMBL_search_drugs`*

Evidence Grading

All Drug Candidates Must Have

  • Evidence tier assigned (★★★ to ☆☆☆)
  • Docking score (if docked)
  • Clinical evidence level
  • Rationale for ranking

Tier Definitions

Tier Symbol Criteria
T1 ★★★ FDA approved for this pathogen
T2 ★★☆ Clinical trial data OR approved for related pathogen
T3 ★☆☆ In vitro activity OR strong docking + mechanism
T4 ☆☆☆ Computational prediction only

Quantified Minimums

Section Minimum Requirement
Related pathogens ≥3 with drug precedent
Druggable targets ≥5 ranked targets
Target details Top 3 with full profiles
Structure predictions ≥3 targets predicted
Drug candidates ≥20 screened
Docking results Top 10 docked
Clinical trials All active trials listed
Recommendations ≥3 immediate actions

Pathogen-Specific Checks

Viral Pathogens

  • Genome type noted (DNA/RNA, ss/ds, +/-)
  • Polymerase identified as target
  • Protease(s) identified
  • Entry mechanism proteins noted
  • Polymerase inhibitors screened
  • Protease inhibitors screened

Bacterial Pathogens

  • Gram stain classification
  • Essential metabolic pathways identified
  • Antibiotic resistance genes checked
  • Cell wall synthesis targets noted
  • Protein synthesis targets noted
  • DNA replication targets noted

Drug-Resistant Pathogens

  • Resistance mechanisms documented
  • Drugs avoiding resistance prioritized
  • Novel mechanism drugs highlighted
  • Combination strategies considered

Docking Quality Checks

Structure Quality

  • Mean pLDDT >70 for docking
  • Active site pLDDT >80
  • No major clashes in structure
  • Binding pocket well-defined

Docking Results

  • Reference drug docked for validation
  • Score interpretation provided
  • Pose quality assessed
  • Binding mode plausible

Output Files

Required

  • [PATHOGEN]_outbreak_intelligence.md - Main report

Recommended

  • [PATHOGEN]_drug_candidates.csv - All candidates with scores
  • [PATHOGEN]_target_proteins.csv - Target list with properties

CSV Column Requirements

drug_candidates.csv:

Drug_Name,ChEMBL_ID,Indication,FDA_Status,Docking_Score,Evidence_Tier,Mechanism

target_proteins.csv:

Target_Name,UniProt_ID,Function,Essentiality,Conservation,Druggability_Score,Drug_Precedent

Urgent Findings Protocol

If any of these found, flag prominently:

  • No approved drugs available
  • All existing drugs ineffective (docking)
  • High mortality/transmission
  • Drug resistance detected
  • Novel pathogen (no related drugs)

Urgent Flag Format

⚠️ **URGENT: [Finding]** ⚠️

[Description of critical finding]

**Recommended Action**: [Immediate step]

Final Review

Before Delivery

  • No [Analyzing...] placeholders remaining
  • All tables properly formatted
  • Executive summary synthesizes key findings
  • Top drug candidate clearly stated
  • Recommendations are actionable and specific
  • Appropriate urgency conveyed

Common Issues to Avoid

  • Targets without UniProt IDs
  • Structures without pLDDT confidence
  • Drugs without FDA status
  • Docking without reference compound
  • Recommendations without evidence support
  • Missing pathogen classification

Speed Optimization

For outbreak scenarios, prioritize:

  1. FDA-approved drugs first (fastest to deploy)
  2. Drugs in phase 3 trials second
  3. Novel candidates last (longest timeline)

Parallel Processing

  • Run taxonomy AND protein searches in parallel
  • Run multiple structure predictions in parallel
  • Dock multiple candidates simultaneously