STRING Database MCP Server
org.string-db/string-mcp · v1.0.0 · MCP 2025-06-18
Query STRING interactions, enrichment, annotations, homology, and PPI networks.
Reachability
reachable
checked 2026-07-14 03:28 UTC
Registry status active
Tools pinned 17
ba2161d448db
Tools last changed
unchanged since first capture 2026-07-14
Provenance
Registry namespace org.string-db
(domain verified by the official registry)
Repository
github.com/meringlab/string-mcp
Website
https://mcp.string-db.org/
Remote endpoints
https://mcp.string-db.org/ (streamable-http)
Observed changes
| When (UTC) | Event | Detail |
|---|---|---|
| 2026-07-14 03:28 | first capture | 17 tools pinned |
Pinned tool definitions (17)
| Tool | Description |
|---|---|
| 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,... |
| 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 'complex' use 'physical' network... |
| 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... |
| 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... |
| 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 step to ensure consistency. If the... |
| 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... |
| 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... |
| 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_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... |
| 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,... |
| 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 by chance). - The enrichment is... |
| 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... |
| 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... |
| 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... |
| 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... |
| 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... |
Status badge
[](https://toolpin.dev/servers/org.string-db/string-mcp)
Maintain this server? Add the badge to your README — it links your users to this live status page.