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MCP live MCP 2025-11-25 http

STRING Database MCP Server

org.string-db/string-mcp

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

Uptime
100.0%
1 direct probes · 30d
Response
249ms
last probe
Tools
17
callable
Resources
0
readable
Prompts
0
available
Primary URL
https://mcp.string-db.org/mcp

Tools · 17

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 transla…

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. If user asks for 'physical' or '…

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**. - U…

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: inclu…

string_network_clustering

Performs **network clustering** on a STRING interaction network and returns both a **network image URL** and details about each detected cluster. Use the same parameters as in the network creation st…

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: include…

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 specie…

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,…

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; enric…

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 …

string_enrichment_image_url

Retrieves the STRING enrichment figure image *URL* for a set of proteins.

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 …

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 cro…

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…

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…

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, enrichm…

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) - functiona…

How to use

Add to your Claude Desktop / Cursor / Cline MCP config:

{
  "mcpServers": {
    "string_database_mcp_server": {
      "url": "https://mcp.string-db.org/mcp",
      "transport": "http"
    }
  }
}