PDB MCP Server

MCP server fronting the RCSB Protein Data Bank — experimental structures, validation reports, and UniProt cross-references. Three community servers are catalogued here: a local REST-based server (Augmented Nature), a hosted GraphQL server (QuentinCody), and a multi-provider server orchestrating RCSB PDB + PDBe + UniProt (cyanheads).

   
Type MCP server
Supplier Augmented Nature · QuentinCody · cyanheads (community OSS)
Availability GA — all actively published; Augmented Nature on mcpservers.org/LobeHub, QuentinCody on Cloudflare Workers, cyanheads in the official MCP Registry
Pricing Free / OSS
Capabilities Read-only

How to install

  • Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/structural-biology-drug-discovery/pdb-database into ~/.claude/skills/).

Option A — Augmented Nature (local, REST, fixed tool set). Clone and build:

git clone https://github.com/Augmented-Nature/PDB-MCP-Server
cd PDB-MCP-Server
npm install
npm run build

Then add to claude_desktop_config.json (replace /path/to/PDB-MCP-Server with the absolute path of your clone — e.g., /Users/you/repos/PDB-MCP-Server, or $(pwd) if you’re still inside it from the previous step):

{
  "mcpServers": {
    "pdb-server": {
      "command": "node",
      "args": ["/path/to/PDB-MCP-Server/build/index.js"]
    }
  }
}

For Claude Code, the equivalent registration is (stdio — Claude launches the process itself, no separate terminal needed):

claude mcp add --transport stdio pdb-server -- node /path/to/PDB-MCP-Server/build/index.js

Option B — cyanheads (multi-provider, RCSB PDB + PDBe + UniProt). Published to npm as protein-mcp-server; requires Bun ≥ 1.2.0. No clone needed. Register with Claude Code over stdio (Claude launches the process itself — no separate terminal needed):

claude mcp add --transport stdio protein-mcp-server --env MCP_TRANSPORT_TYPE=stdio -- bunx protein-mcp-server@latest

For Claude Desktop, add the equivalent stdio entry to claude_desktop_config.json:

{
  "mcpServers": {
    "protein-mcp-server": {
      "command": "bunx",
      "args": ["protein-mcp-server@latest"],
      "env": { "MCP_TRANSPORT_TYPE": "stdio" }
    }
  }
}

(The server defaults to HTTP on port 3010; setting MCP_TRANSPORT_TYPE=stdio forces stdio so Claude Desktop, which has no native HTTP transport, can launch it directly.)

Option C — QuentinCody (hosted, GraphQL). This server is deployed on Cloudflare Workers; nothing to build or keep running locally. Register the remote endpoint with Claude Code:

claude mcp add --transport sse rcsb-pdb https://rcsb-pdb-mcp-server.quentincody.workers.dev/sse

For Claude Desktop (no native SSE transport), use an mcp-remote proxy entry in claude_desktop_config.json:

{
  "mcpServers": {
    "rcsb-pdb": {
      "command": "npx",
      "args": ["mcp-remote", "https://rcsb-pdb-mcp-server.quentincody.workers.dev/sse"]
    }
  }
}

What it does

Augmented Nature (REST) — fixed tool set:

  • search_structures
  • get_structure_info
  • download_structure (PDB / mmCIF / mmTF / XML)
  • search_by_uniprot
  • get_structure_quality

QuentinCody (GraphQL) — exposes the RCSB Data API’s GraphQL endpoint so Claude composes arbitrary queries: entry metadata, experimental method, molecules/sequences, and Computed Structure Models (CSMs).

cyanheads (multi-provider) — orchestrates RCSB PDB, PDBe, and UniProt behind a unified tool set:

  • protein_search_structures — keyword/filter search with pagination
  • protein_get_structure — full structure data by PDB ID
  • protein_find_similar — structural / sequence homologs
  • protein_track_ligands — find structures binding a given small molecule
  • protein_compare_structures / protein_analyze_collection — comparison and database statistics (marked in development upstream)

Primary use cases: Pull experimental 3D structures into Claude workflows; map UniProt to PDB; assess structure validation quality before downstream modeling; flexible GraphQL queries over PDB metadata and computed models.

Notes

The Augmented Nature server is Node/stdio, no auth, calls the public RCSB REST API; its LICENSE file is present but type unspecified in the README — verify before redistributing. The QuentinCody server is a hosted Cloudflare Worker (MIT License with an academic-citation requirement) and exposes a single GraphQL query surface rather than discrete typed tools. The cyanheads server is Apache-2.0, requires Bun ≥ 1.2.0, needs no API key by default (supports optional JWT/OAuth modes), and supports both HTTP (default, port 3010) and stdio transports. All three are read-only.

Sources

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