STRING Database MCP Server

Name: STRING Database MCP Server
Author: meringlab

by meringlabversion 1.13.1i★ –iRuns in the cloud

Registry nameorg.string-db/string-mcp

Install

Overview

Description from the maker (original English)

Query STRING interactions, enrichment, annotations, homology, and PPI networks.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi0 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs in the cloud
Transport: Streamable HTTP
Category: Databases & datasets

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 0 of 1 passed
Runs on the maker’s server: what you ask it goes through their server.
The registry lists no key to fill in.

You need

Runs in the cloudNothing to install; it connects over the internet

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Works in Claude on the web, desktop and mobile:

Open Settings → Connectors
Press Add custom connector
Paste the address below and press Add
If it asks you to sign in, sign in with the maker

https://mcp.string-db.org/

Run this in your terminal

claude mcp add --transport http string https://mcp.string-db.org/

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "string": {
      "url": "https://mcp.string-db.org/"
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "string": {
      "type": "http",
      "url": "https://mcp.string-db.org/"
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

ChatGPT connects only to servers on the internet:

Open ChatGPT on the web → Settings → Connectors (Apps)
Press Create or Add (some plans need Developer mode under Advanced first)
Paste the address below, give it a name and save
If it asks you to sign in, sign in with the maker

https://mcp.string-db.org/

Menu names can differ slightly by plan and over time.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

We have not read this server’s tool list yet; we check endpoints in rotation.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 7, 2026

! Caution
Maker matches the repo
The publisher (string-db.org) is not the repo owner (meringlab); someone else may have listed it
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
… Not checked yet
Endpoint responds
Not checked yet; we check endpoints in rotation
… Not checked yet
Sign-in with OAuth
Not checked yet; we check endpoints in rotation
… Not checked yet
No hidden instructions in tool descriptions
Not checked yet; we read the tool list when we check the endpoint

Compared with others in Databases & datasetsi

More stars than 0% of the other 953 servers in this category
Published to the registry more recently than 80% of the other 953 servers in this category
Basic checks equal to or better than 39% of the other 953 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is STRING Database MCP Server safe?

It passed 0 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs in the maker’s cloud. Connect over the internet with nothing to install, but what you send passes through the maker’s servers.

Is it still maintained?

The GitHub repo last changed –, and the latest version (1.13.1) reached the registry 10 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.

What can I use instead?

In the same category: Supabase, MongoDB MCP Server, Elasticsearch MCP Server

Alternatives

Servers in the same category from other makers, sorted by stars.

Reading a card:★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

Supabase

by supabase

Supabase’s official server lets AI create tables, query data and review project settings in your Supabase database.

Computer or cloud★ 2,993Apache-2.0Updated today

Install

MongoDB MCP Server

by mongodb-js

MongoDB Model Context Protocol Server

Runs on your computer★ 1,157Apache-2.0Updated 2 days ago

Install

Elasticsearch MCP Server

by cr7258

MCP server for interacting with Elasticsearch

Runs on your computer★ 315Apache-2.0Updated 14 months ago

Install

README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

Official STRING Database MCP Server

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 workflows, use the optional agent skill at skills/string-database/SKILL.md.

Features

Resolve protein identifiers to STRING metadata
Retrieve interaction networks
Cluster and visualize interaction networks
Perform homology lookups across species
Access evidence links for protein–protein interactions
Run functional enrichment analysis (including enrichment plots)
Get curated functional annotations for proteins
Query proteins by function or disease (GO, KEGG, Reactome, DISEASES etc.)

Requirements

Python ≥ 3.11 (with Python 3.10, optional parameter descriptions are misplaced in the tool schemas)
Dependencies (see requirements.txt):
fastmcp==2.14.7
mcp==1.29.0
httpx>=0.28,<0.29
pydantic>=2.11,<3.0

Note: If the server crashes on startup, it is very likely due to an incompatible FastMCP version.

Configuration

The server reads settings from config/server.config (JSON). Example:

"base_url": "https://string-db.org", "server_port": 57416, "verbosity": "low" }

Installation

git clone https://github.com/meringlab/string-mcp.git

cd string-mcp pip install -r requirements.txt

Running

python server.py

To serve over standard input/output instead of HTTP, for example when a local MCP client starts the server itself:

python server.py --stdio

The stdio mode also reads config/server.config for the STRING API endpoint.

Testing

   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.

Docker

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.

Frozen STRING releases are available under versioned paths: /12.0/ (STRING v12.0) and /12.5/ (STRING v12.5).

License / Citation

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.

STRING Database MCP Server

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Databases & datasetsi

Common questions

Alternatives

Supabase

MongoDB MCP Server

Elasticsearch MCP Server

README from the maker

Official STRING Database MCP Server

Features

Requirements

Configuration

Installation

Running

Testing

Docker

Windows PowerShell

License / Citation