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STRING Database MCP Server

MCP serverVerified domain · string-db.orgRemote● LiveFree to try

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

Install

Remote server: your requests and data go to mcp.string-db.org. Claude Code: claude mcp add --transport http string-database-mcp-server https://mcp.string-db.org/ · Claude app: Settings → Connectors → Add custom connector.

What it can do

The tools this server listed when we connected to it, in its own words.

  • string_resolve_proteins — Maps one or more protein identifiers to their corresponding STRING metadata, including: gene symbol, description, sequence, domains, species
  • 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
  • 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
  • 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
  • string_network_clustering — Performs **network clustering** on a STRING interaction network and returns a network image URL, an interactive STRING network URL, and deta
  • 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 1
  • string_homology — Retrieves pairwise protein similarity scores (Smith–Waterman bit scores) for the query proteins. - If no target species (`species_b`) is pro
  • 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 i
  • 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
  • string_functional_annotation — This tool retrieves curated functional annotations for a set of proteins. Each input protein is mapped to known biological terms from ontolo
  • 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`. - Ea
  • 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
  • string_proteins_for_term — Retrieve proteins annotated with a functional term or descriptive text in a single species. You can query for tissues, compartments, disease
  • string_sequence_search — Searches the STRING database using **amino acid sequences** to identify matching proteins. - Accepts a single sequence or multiple sequences
  • 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
  • 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
  • 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

KitScout test notes

Not tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.

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