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.

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

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.

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").