STRING Database MCP Server

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.

You need

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

Which app do you use?

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

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

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

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

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

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

Tool names and descriptions exactly as the server reported them on Nov 7, 2026. The maker wrote them, not us; we show them as plain text.

• string_resolve_proteins

  Maps one or more protein identifiers to their corresponding STRING metadata, including: gene symbol, description, sequence, domains, species, and internal STRING ID. This method is useful for translating raw identifiers into readable, annotated protein entries. Example input: "TP

• string_interactions_query_set

  Retrieves the interactions between the query proteins. Use this method only when you specifically need to list the interactions between all proteins in your query set. - For a **single protein**, the network includes that protein and its top 10 most likely interaction partners, p

• string_all_interaction_partners

  Retrieves all interaction partners for one or more proteins from STRING. This tool returns all known interactions between your query protein(s) and **any other proteins in the STRING database**. - Use this when asking **“What does TP53 interact with?”** - It differs from `string_

• string_visual_network

  Retrieves a URL to a **STRING interaction network image** for one or more proteins. - For a single protein: includes the protein and its top 10 most likely interactors. - For multiple proteins: includes all known interactions **within the query set**. The input may include one nu

• string_network_clustering

  Performs **network clustering** on a STRING interaction network and returns a network image URL, an interactive STRING network URL, and details about each detected cluster. Provide a table with each detected cluster’s color, STRING-derived functional description, and any returned

• string_network_link

  Retrieves a stable URL to an interactive STRING network for one or more proteins. - For a single protein: includes the protein and its top 10 most likely interactors. - For multiple proteins: includes all known interactions **within the query set**. The input may include one nume

• string_homology

  Retrieves pairwise protein similarity scores (Smith–Waterman bit scores) for the query proteins. - If no target species (`species_b`) is provided, results are intra-species (within the query species). - To retrieve homologs in other species or clades (e.g. vertebrates, yeast, pla

• string_interaction_evidence

  Retrieves direct links to STRING evidence pages for protein–protein interaction pairs. Use this tool only when a STRING evidence page/link is needed. To determine whether an interaction is supported, use `string_interactions_query_set`. It returns URLs linking to STRING’s evidenc

• string_enrichment

  This tool retrieves functional enrichment for a set of proteins using STRING. - If queried with a single protein, the tool expands the query to include the protein’s 10 most likely interactors; enrichment is performed on this set, not the original single protein. - For two or mor

• string_functional_annotation

  This tool retrieves curated functional annotations for a set of proteins. Each input protein is mapped to known biological terms from ontologies, pathway databases, tissues, compartments and domains — such as Gene Ontology (GO), KEGG, and UniProt Keywords. - Use this when the use

• string_enrichment_image_url

  Retrieves a STRING enrichment figure (image URL) for a set of proteins. For the enriched terms and FDR values, use `string_enrichment`. - Each figure shows a single enrichment category; call again with another `category` to show a different one. - Use the same proteins and specie

• string_ppi_enrichment

  This tool tests if your network is enriched in protein-protein interactions compared to the background proteome-wide distribution (i.e., if your proteins are more functionally connected than expected by chance). - The enrichment is assessed using the actual observed edges versus

• string_proteins_for_term

  Retrieve proteins annotated with a functional term or descriptive text in a single species. You can query for tissues, compartments, diseases, processes, pathways, and domains. IMPORTANT: For cross-species comparisons, run this tool separately for each species. Select relevant mo

• string_sequence_search

  Searches the STRING database using **amino acid sequences** to identify matching proteins. - Accepts a single sequence or multiple sequences in FASTA format. - Returns the most similar STRING protein(s) for the specified species, based on sequence similarity. - Use this when the

• string_query_species

  Search for species or clades available in STRING by free-text query and return their NCBI taxonomy IDs. - Use this when the user asks which species or clades are present in STRING, or when you need the correct NCBI taxon ID to pass to other tools. - use this to resolve NCBI taxon

• string_create_file

  Creates a downloadable file for STRING-derived results. Use this tool when the user explicitly asks to download, save, export, or receive a file containing STRING data, tables, protein lists, enrichment results, networks, etc. When a response would otherwise include a publication

• string_help

  Provides explanatory text for STRING features and limitations. Use this tool when the user question involves: - What is STRING is or how to use the tool (how_to_use_string, cytoscape) - functionality not available via MCP tools (e.g. GSEA or large datasets). - meaning of network

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

• ✓ Pass

  Endpoint responds

  Responded in 862 ms (HTTP 200)

• – Not applicable

  Sign-in with OAuth

  No sign-in needed

• ✓ Pass

  No hidden instructions in tool descriptions

  Read 17 tool descriptions and found no hidden instructions to the AI

Compared with others in Databases & datasetsi

• More stars than 0% of the other 954 servers in this category
• Published to the registry more recently than 80% of the other 954 servers in this category
• Basic checks equal to or better than 42% of the other 954 servers in this category

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

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

README from the maker

{

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

python server.py

python server.py --stdio

   curl -v -H "Accept: text/event-stream" http://localhost:[port]/mcp

   cp config/server.config.example config/server.config

   docker build -t string-mcp .

   docker run -p 57416:57416 -v $(pwd)/config:/app/config:ro string-mcp

   docker run -p 57416:57416 -v ${PWD}/config:/app/config:ro string-mcp

   docker run -p 57416:57416 -v %cd%/config:/app/config:ro string-mcp

   # Linux/macOS

   docker stop string-mcp-server