by-database

Skill: by-database

Use the BY MCP database tools to query PDB, UniProt, and SAbDab for target characterization, antibody scaffold selection, and competition analysis.

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When to Use This Skill

Use this skill when you need:

• ✅ Structural metadata for a target (resolution, method, organism, chains)
• ✅ Interface residue lists for hotspot selection in PXDesign / BoltzGen
• ✅ Canonical UniProt sequence, domain boundaries, or known variants
• ✅ Existing antibody-antigen complexes for scaffold selection or competition analysis
• ✅ Cross-referencing PDB residue numbering with UniProt positions
• ✅ Verifying chain composition before generating a design spec

Don't use this skill for:

• ❌ Full target research narrative or literature review → use by-research
• ❌ Epitope hotspot scoring or surface analysis → use by-epitope-analysis
• ❌ Scoring designs (ipSAE, ipTM, liabilities) → use by-scoring / by-screening
• ❌ Web search or PubMed lookups → fall back to PubMed/bioRxiv tools then WebSearch
• ❌ Submitting compute jobs → use boltzgen, pxdesign, protenix skills

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Quick Start

Look up a target end-to-end in three calls:

mcp__by-pdb__pdb_search(query="PD-L1", max_results=10)
mcp__by-uniprot__uniprot_search(query="CD274 human", max_results=5)
mcp__by-sabdab__sabdab_search_by_antigen(antigen_name="PD-L1", max_results=20)

For batch enrichment of a known list of PDB IDs without an MCP loop:

python scripts/batch_pdb_lookup.py --ids 7S4S 6XWG 5JDS --out enriched.csv

✅ VERIFICATION: Expect ✓ batch_pdb_lookup completed: 3 rows -> enriched.csv.

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Inputs

Required (at least one of):

• PDB ID — 4-character RCSB identifier (e.g. 7S4S). Source: mcp__by-pdb__pdb_search.
• UniProt accession — e.g. Q9NZQ7. Source: mcp__by-uniprot__uniprot_search.
• Target name / gene symbol — e.g. "PD-L1", "CD274". Used as free-text query.
• Antigen name — for SAbDab antibody lookups (e.g. "HER2").