by-research

BY Research Skill

Thorough target research before design prevents wasted compute and failed campaigns. This skill defines an 8-phase pipeline that retrieves, validates, and packages research findings with quality gates and anti-drift checkpoints at every stage.

When to Use This Skill

Use this skill when you have:

• ✅ A protein target name or identifier (UniProt accession, gene name, PDB ID, or common name)
• ✅ A new design campaign starting — research is always step 1 before planning
• ✅ A need to characterize prior art — existing antibodies, nanobodies, or designed binders
• ✅ A target with unknown or partially characterized epitopes — needs hotspot identification from literature + structure
• ✅ A need to choose modality or scaffold — research informs VHH vs scFv vs de novo
• ✅ An interrupted research session — resume from research_progress.json checkpoint

Do NOT use this skill when:

• ❌ You already have a validated target report in the campaign directory → load it instead of re-researching
• ❌ You are scoring or filtering existing designs → use by-scoring or by-screening
• ❌ You are predicting structure of a known sequence → use Protenix directly (no literature needed)
• ❌ You need lab submission logistics → use by-deploy-compute or the lab-submission flow
• ❌ The user wants ranked design results → use by-display / results skill
• ❌ You need a one-off database lookup (single PDB fetch) → call the MCP tool directly, no 8-phase overhead

Quick Start

User: "Research TNF-alpha for a nanobody design campaign."

Agent:
  1. Phase 1 SCOPE  → writes research/scope.json (target=TNF-alpha, modality=VHH, depth=quick)
  2. Phase 2 PLAN   → writes research/research_plan.json
  3. Phase 3 RETRIEVE → calls 4 research_* MCP tools in parallel, writes sources.json
  4. Phase 4 TRIANGULATE → writes validated_findings.json
  5. Phase 5 SYNTHESIZE → drafts research.md
  6. Phase 6 CRITIQUE  → 3 personas, writes critique.json
  7. Phase 7 REFINE   → closes gaps, updates sources.json + validated_findings.json
  8. Phase 8 PACKAGE  → writes research.md + recommended_hotspots.json + design_recommendation.json

Expected: 10-15 sources, 3+ HIGH confidence findings, 5-10 hotspot residues,
         design_recommendation.json with modality/protocol/tier ready for campaign-manager.