search_structuresLABSCO 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.
Setup effort
Build from source — git clone https://github.com/Augmented-Nature/PDB-MCP-Server.git
USE CASES
01
Finding structures for a protein you are working on
Search by name or keyword and see what has actually been solved.
02
Going from a UniProt accession to solved structures
Look up every PDB entry associated with the accession, without translating identifiers by hand.
03
Judging whether a structure is good enough to build on
Read the validation metrics next to the structure's own detail before committing to it.
04
Getting coordinates into your own pipeline
Download in PDB, mmCIF, mmTF or XML, whichever the next tool in the chain expects.
5 tools
Listed in project docs. Your client may show a different list.
get_structure_infodownload_structuresearch_by_uniprotget_structure_qualityBEFORE YOU INSTALL
What to know first
Tools you get
5 tools named in the project's documentation.
Where it runs
The documented client runs the server on your machine.
INSTALLATION
Connect your client
You clone and build this one yourself.
Server setup
TERMINAL
git clone https://github.com/Augmented-Nature/PDB-MCP-Server.git
cd PDB-MCP-Server
npm install
npm run buildMCP Clients
Any MCP client
ANY MCP CLIENT · JSON
{
"mcpServers": {
"pdb-server": {
"command": "node",
"args": [
"<YOUR_PATH_TO_PDB_MCP_SERVER>/build/index.js"
]
}
}
}
