Labsco
MCP SERVER

PDB MCP Server

by Augmented-Nature ↗

Find the structures for a target, judge their quality, and download coordinates in the format your tool reads.

Biomedical: Genomics & Clinical Data
Summary
Structure lookup that ends with the file, not a link to it.

Search, detail and validation in one place, and the coordinates themselves in whichever of four formats your downstream tool wants. The UniProt route saves the most time: accession in, solved structures out.

What it is

A Node MCP server over the RCSB Protein Data Bank, built on its data, search and file-download APIs. Five tools, plus a pdb:// resource scheme for structures, coordinates, mmCIF, validation data and ligands.

What you get
  • The PDB searched by keyword, protein name or PDB ID
  • Full detail for a specific structure
  • Coordinates downloaded as PDB, mmCIF, mmTF or XML
  • Structures found from a UniProt accession, so you can go from sequence to structure
  • Quality metrics and validation data for a structure
  • Structures, coordinates, validation and ligand data also addressable as pdb:// resources
Requirements

Node, with npm install and npm run build, then point your client at the built index.js. No key or account — it reads the public RCSB data, search and download endpoints.