STRING Database MCP: protein interaction queries in your AI app

Add STRING to Claude, ChatGPT or Cursor

1. 1Click Connect STRING Database free. There's no sign-in, so its tools are ready at once.
2. 2The tools query STRING and return data, images or links. `string_create_file` creates downloadable files; switch it off if you only want answers in the chat, and keep the query tools on.
3. 3Add ContextGate to your AI app as a connector or MCP server. The steps for each app are on the Works with page.
4. 4Ask your AI app for the interaction partners of TP53 in human, with a network image, then open Activity to see the calls.

Protein network work in a chat

• Map protein identifiers to STRING metadata, from gene symbol to domains and species, with `string_resolve_proteins`.
• List every known interaction partner of a protein with `string_all_interaction_partners`.
• Run functional enrichment on a protein set with `string_enrichment`, or test a network for PPI enrichment with `string_ppi_enrichment`.
• Get a network image URL from `string_visual_network`, or cluster a network with `string_network_clustering`.
• Search STRING by amino acid sequence in FASTA format with `string_sequence_search`.

That's 7 of STRING's 17 tools; the rest, including homology and species search, are listed as soon as you connect.

A record for your methods section

• Activity keeps every STRING query, so you can retrace which proteins and species an analysis used.
• Switch off tools you don't use, such as `string_create_file`, and they're hidden from your AI app.

What you get with STRING Database and ContextGate

• Your AI apps can use STRING DatabaseClaude, Cursor, ChatGPT and other AI apps reach STRING Database through the one ContextGate connection you add to them.
• You choose which tools they can useSwitch off any STRING Database tool you don't want used. It's hidden from your AI apps and refused if called.
• Every call is checked and recordedYour policies check each call (for example, personal data is hidden and secrets are blocked), and Activity keeps a record of it.

ContextGate sees only the tool calls that go through it, not your AI app's built-in tools or your chats.

STRING Database tools

Examples of what your AI apps can do in STRING Database. You'll see the exact list of tools after you connect it.

• string_resolve_proteinsMaps one or more protein identifiers to their corresponding STRING metadata, including: gene symbol, description, sequence, domains, species, and internal STRIN
• string_interactions_query_setRetrieves the interactions between the query proteins. Use this method only when you specifically need to list the interactions between all proteins in your que
• string_all_interaction_partnersRetrieves all interaction partners for one or more proteins from STRING. This tool returns all known interactions between your query protein(s) and **any other
• string_visual_networkRetrieves 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 int
• string_network_clusteringPerforms **network clustering** on a STRING interaction network and returns a network image URL, an interactive STRING network URL, and details about each detec
• string_network_linkRetrieves 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 inter
• string_homologyRetrieves pairwise protein similarity scores (Smith–Waterman bit scores) for the query proteins. - If no target species (`species_b`) is provided, results ar
• string_interaction_evidenceRetrieves direct links to STRING evidence pages for protein–protein interaction pairs. Use this tool only when a STRING evidence page/link is needed. To determ
• string_enrichmentThis 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 pro
• string_functional_annotationThis tool retrieves curated functional annotations for a set of proteins. Each input protein is mapped to known biological terms from ontologies, pathway datab
• string_enrichment_image_urlRetrieves 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 s
• string_ppi_enrichmentThis tool tests if your network is enriched in protein-protein interactions compared to the background proteome-wide distribution (i.e., if your proteins are mo
• string_proteins_for_termRetrieve proteins annotated with a functional term or descriptive text in a single species. You can query for tissues, compartments, diseases, processes, path
• string_sequence_searchSearches the STRING database using **amino acid sequences** to identify matching proteins. - Accepts a single sequence or multiple sequences in FASTA format. -
• string_query_speciesSearch 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 a
• string_create_fileCreates a downloadable file for STRING-derived results. Use this tool when the user explicitly asks to download, save, export, or receive a file containing STR
• string_helpProvides 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