@pipeworx/rcsb-pdb

Connect: https://gateway.pipeworx.io/rcsb-pdb/mcp · Install: one-click buttons

Tools: 6

RCSB Protein Data Bank MCP — 3-D structure metadata for ~225 k experimentally determined macromolecules. Keyless.

Tools

• search(query, return_type?, limit?) — text search across PDB
• structure(pdb_id) — full entry record (experiment, ligands, polymer entities)
• polymer_entity(pdb_id, entity_id) — single polymer entity (chain) metadata
• ligand(pdb_id, ligand_id) — ligand record
• assembly(pdb_id, assembly_id?) — biological assembly
• summary(pdb_id) — short summary view

Data sources

• Search: https://search.rcsb.org/rcsbsearch/v2/query
• Data: https://data.rcsb.org/rest/v1/core/

Tools

• search — Text search across PDB. Returns matching PDB IDs.
• structure — Full entry record by PDB ID (e.g. “1abc”).
• polymer_entity — Polymer-entity (chain) metadata.
• ligand — Non-polymer ligand record (e.g. cofactor, drug).
• assembly — Biological assembly (defaults to “1” — the first/canonical).
• summary — Short entry summary.