STRING Database MCP Server — Claude Code MCP server: STRING access
Lets an agent pull protein interaction networks, enrichment results, annotations and homology lookups from STRING. Handy when you want to work through PPI data inside the chat.
claude mcp add --transport http string-mcp https://mcp.string-db.org/What STRING Database MCP Server does
The server wraps the STRING API in an MCP interface. An agent gets tools to resolve protein identifiers, fetch interaction networks, cluster and visualize them, look up homologs across species, and run functional enrichment with plots. Curated annotations and queries by function or disease are covered too, through GO, KEGG, Reactome and DISEASES.
Under the hood it is a Python server built on FastMCP. You need Python 3.11 or newer — on 3.10 the optional parameter descriptions land in the wrong place in the tool schemas. Dependencies live in requirements.txt: fastmcp==2.14.7, mcp==1.29.0, httpx>=0.28,<0.29, pydantic>=2.11,<3.0. A crash at startup usually means a mismatched FastMCP version. Settings come from config/server.config as JSON, covering the API base URL, port and verbosity.
Two ways to run it. Locally: clone the repo, install the dependencies, start python server.py, or use python server.py --stdio when the MCP client launches the process itself. Otherwise point your client at the hosted endpoint https://mcp.string-db.org and keep nothing on your machine. The hosted route is less work, though every query leaves your machine.
What it helps with
- pull an interaction network for a set of proteins
- find homologs of a protein in another species
- run functional enrichment and get a plot
- check the evidence behind a protein–protein link
- search proteins by disease or function
Example prompts for the agent
- Resolve these protein identifiers in STRING and show their metadata
- Build the interaction network for this gene list and cluster it
- Run GO and KEGG enrichment on this set of proteins
How to install STRING Database MCP Server
Platform CLI: remote server
claude mcp add --transport http string-mcp https://mcp.string-db.org/Platform CLI: remote server
codex mcp add string-database-mcp-server --url https://mcp.string-db.org/Config file
{
"mcpServers": {
"string-database-mcp-server": {
"url": "https://mcp.string-db.org/"
}
}
}Config file
{
"servers": {
"string-database-mcp-server": {
"type": "http",
"url": "https://mcp.string-db.org/"
}
}
}Platform CLI: remote server
gemini mcp add -t http string-database-mcp-server https://mcp.string-db.org/Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about STRING Database MCP Server
How do I install STRING Database MCP Server in Claude Code?
Add the hosted endpoint: claude mcp add --transport http string-mcp https://mcp.string-db.org/. For a local setup, clone the repo, run pip install -r requirements.txt and start python server.py.
What does STRING Database MCP Server do?
It exposes STRING database features to an agent: protein interaction networks, clustering and visualization, homology lookups, evidence links for interactions, enrichment analysis and curated annotations.
What do I need to run it locally?
Python 3.11 or newer plus the dependencies in requirements.txt. Configuration sits in config/server.config; when the client starts the server itself, launch python server.py --stdio.
