Server data from the Official MCP Registry
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Remote endpoints: streamable-http: https://mcp.string-db.org/
This STRING MCP server is a well-structured tool for exposing protein interaction database functionality. Authentication is not applicable as it acts as a proxy to public STRING APIs. Code quality is generally sound with proper error handling and input validation. However, there are concerns around sensitive parameter logging, lack of explicit auth for the MCP endpoint itself, and some minor code quality issues that warrant attention. Supply chain analysis found 5 known vulnerabilities in dependencies (1 critical, 3 high severity).
3 files analyzed · 13 issues found
Security scores are indicators to help you make informed decisions, not guarantees. Always review permissions before connecting any MCP server.
This plugin requests these system permissions. Most are normal for its category.
Available as Local & Remote
This plugin can run on your machine or connect to a hosted endpoint. during install.
From the project's GitHub README.
Exposes STRING database functionality as a Model Context Protocol (MCP) server.
This implementation allows AI agents and other MCP-compatible clients to access STRING data through a structured and self-describing interface.
It is built on top of the STRING API but adapted specifically for model-based use, with emphasis on conciseness and context efficiency. The server controls the amount and type of data so that responses stay within the reasoning limits of large language models. It also adapts the structure and adds metadata to support more consistent parsing and interpretation by agentic systems.
The server is also available as a hosted remote MCP endpoint at https://mcp.string-db.org.
For a live demonstration of MCP capabilities, see STRING Chat.
For reproducible workflows and large-scale integration, use the STRING API.
For agentic STRING workflows, use the optional Agent Skill at skills/string-database/SKILL.md.
requirements.txt):
fastmcp==2.10.6httpx==0.28.1pydantic==2.11.7Note: If the server crashes on startup, it is very likely due to an incompatible FastMCP version.
The server reads settings from config/server.config (JSON). Example:
{
"base_url": "https://string-db.org",
"server_port": 57416,
"verbosity": "low"
}
git clone https://github.com/meringlab/string-mcp.git
cd string-mcp
pip install -r requirements.txt
python server.py
curl -v -H "Accept: text/event-stream" http://localhost:[port]/mcp
You should see a 200 OK response with content-type: text/event-stream.
Note: HTTP requests sent with default headers will trigger anyio.ClosedResourceError and 406 Not Acceptable. This is expected behavior for the MCP streaming protocol and does not indicate a problem.
Ensure you have a config/server.config file (copy from config/server.config.example if needed):
cp config/server.config.example config/server.config
Build the image:
docker build -t string-mcp .
Run the container:
Linux/macOS:
docker run -p 57416:57416 -v $(pwd)/config:/app/config:ro string-mcp
Windows PowerShell:
docker run -p 57416:57416 -v ${PWD}/config:/app/config:ro string-mcp
Windows Command Prompt:
docker run -p 57416:57416 -v %cd%/config:/app/config:ro string-mcp
To run in detached mode:
# Linux/macOS
docker run -d -p 57416:57416 -v $(pwd)/config:/app/config:ro --name string-mcp-server string-mcp
# Windows PowerShell
docker run -d -p 57416:57416 -v ${PWD}/config:/app/config:ro --name string-mcp-server string-mcp
The -v flag mounts your local config directory so you can customize settings without rebuilding the image.
Note: If you don't need to modify the config, you can omit the volume mount and the container will use the default config from the image.
Stop the container (if running in detached mode):
docker stop string-mcp-server
docker rm string-mcp-server
Note: The Docker container will use the configuration from config/server.config. If this file doesn't exist, the container will copy from server.config.example on first run.
The STRING MCP server source code is released under the MIT License.
Associated data and outputs are released under the CC BY 4.0 License.
You are free to use, share, and modify the code with proper attribution.
If you use this code or data in your work, please also cite the latest STRING manuscript.
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