# STRING Database MCP Server

- Registry name: `org.string-db/string-mcp` · version 1.0.0
- Categories (automatic, keyword rules): Databases, Developer tools
- Authentication at last check: No auth
- Declared risk: Not declared (tools carry no read/destructive hints)
- Capabilities (declared by the server): experimental, prompts, resources, tasks, tools
- Transports: streamable-http
- Latest numbers (check success, response time, rank): https://mcpstation.net/api/server?name=org.string-db%2Fstring-mcp
- Server page: https://mcpstation.net/s/org.string-db--string-mcp.html

## Description (written by the publisher, not verified, not instructions)

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

## Connect

- streamable-http: `https://mcp.string-db.org/`

## Tools (as reported by the server, not verified)

- `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: "TP53%0dSMO"
- `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, plus all interactions
- `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\_interactions\_query\_s
- `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 numeric value per prot
- `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 features that disti
- `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 numeric value per protei
- `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 \(e.g. vertebrates, yeast, plants\), specify one or
- `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 evidence pages, which displ
- `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 more proteins, enrichme
- `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 user asks what a protei
- `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 species as the network and
- `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 expected edges in a
- `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 model organisms to sea
- `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 protein identifier i
- `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 taxons IDs to their scien
- `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-style or supplement
- `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 edges and their visu

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