MCP server

STRING Database MCP Server

org.string-db/string-mcp

Checked 25 Oct 2026, 20:29 UTC · Connected to it and listed its tools

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

Website Source

At a glance

Type

MCP server

Publisher

string-db.org (verified by the MCP Registry)

Status

Working at last check

Tools

17

Token cost

About 10,346 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

25 Oct 2026, 20:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

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

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.string-mcp]
url = "https://mcp.string-db.org/"

Gemini CLI

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

Cursor

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

VS Code

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

Antigravity

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

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"string-mcp","server_url":"https://mcp.string-db.org/","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"string-mcp","server_url":"https://mcp.string-db.org/"}

Tools

• string_all_interaction_partners ~688 tokens
  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_interactions_query
• string_create_file Changes files · ~413 tokens
  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-style or suppleme
• string_enrichment ~785 tokens
  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 more proteins, enrichm
• string_enrichment_image_url ~660 tokens
  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 species as the network an
• string_functional_annotation ~428 tokens
  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 user asks what a prot
• string_help ~288 tokens
  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 edges and the
• string_homology ~336 tokens
  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, plants), specify o
• string_interaction_evidence ~585 tokens
  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 evidence pages, which dis
• string_interactions_query_set ~878 tokens
  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, plus all interaction
• string_network_clustering ~1259 tokens
  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 features that dist
• string_network_link ~956 tokens
  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 numeric value per prot
• string_ppi_enrichment ~496 tokens
  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 expected edges in a
• string_proteins_for_term ~603 tokens
  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 model organisms
• string_query_species ~307 tokens
  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 taxons IDs to their sc
• string_resolve_proteins ~273 tokens
  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: "TP53%0dSMO"
• string_sequence_search ~267 tokens
  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 protein identifier
• string_visual_network ~1124 tokens
  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 numeric value per pr

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