STRING Database MCP Server

Install

Works with Claude Code, VS Code, Cursor, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install connector/string-db-org-string-mcp

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Permissions

What this server can do and what it asks for, from its tool list, install config and code. Checked Oct 25, 2026.

Tools

12 read · 2 write · 0 delete · 3 not yet classified

Secrets

None asked for

Install scripts

Nothing to install (hosted)

Runs as

Hosted (remote endpoint)

Tools (17)

As the server listed them on Oct 25, 2026. Descriptions are the server’s own words; hidden characters are shown as [U+…].

• string_all_interaction_partnersSTRING: Get all interaction partners for proteins

  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_set`, which only shows interactions **within the input set** or a limited extension of it. You can filter for strong interactions using `required_score`. - Evidence scores: `nscore` (neighborhood), `fscore` (fusion), `pscore` (phylogenetic profile), `ascore` (coexpression), `escore` (…

• string_create_fileSTRING: Create a downloadable STRING result 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 supplementary result table, or another table clearly intended for reuse outside chat, mention that a downloadable TSV/CSV file can be generated on request. Ask whether they want the file, unless they already requested it. Do not create the file until the user asks for it. Do not store unrelated data or ful…

• string_enrichmentSTRING: Functional enrichment analysis

  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, enrichment is performed on the exact input set. - When calling related tools, use the same input parameters unless otherwise specified. - Focus summaries on the top categories and most relevant terms for the results. Always report FDR for each claim. - Report FDR as a human-readable value (e.g. 2.3e-5 or 0…

• string_enrichment_image_urlSTRING: Get enrichment result figure (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 enrichment results already shown to the user, so the figure matches them.

• string_functional_annotationSTRING: Retrieve functional annotations for proteins

  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 protein does, where it's localized, expressed, or which pathways it participates in. - Keep the output short and focused by highlighting a few diverse and specific annotations for each protein. - This tool does not perform statistical enrichment — use the enrichment tool for that. Output fields (per pr…

• string_helpSTRING: Help / FAQ

  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 visual encoding (network_edge_legend) - interpretation of enrichment strength and signal (enrichment_scores) - grouping of terms in enrichment figures (enrichment_grouping)

• string_homologySTRING: Get homologs in specified target species

  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 more NCBI taxon IDs in `species_b`. - Multiple target species are supported; ask the user to clarify if needed. - Always report species names together with their taxon IDs. - Bit scores < 50 are not reported. - Results are truncated to the top 50 proteins per input protein.

• string_interaction_evidenceSTRING: Get links to interaction evidence pages

  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 display the underlying data sources (experimental results, publications, and curated databases) supporting each predicted interaction. A URL can be generated even for unsupported pairs; the URL is not itself an interaction verdict. The returned page lets the user explore functional, physical, and re…

• string_interactions_query_setSTRING: Get interactions within 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 among those partners. - For **multiple proteins**, the network includes all direct interactions between them. - STRING does not store or report information about self-interactions/homomers; if asked, explain the limitation. If few or no interactions are returned, consider reducing the `required_s…

• string_network_clusteringSTRING: Perform 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 distinguish it from the others. Use the same parameters as in the network creation step to ensure consistency. If the network already contains disconnected subgraphs, the resulting number of clusters may differ from the requested value. Inter-cluster edges are faded by default. Use `inter_cluster_edge…

• string_network_linkSTRING: Get interactive network link (web UI)

  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 protein, such as fold change, effect size, or score. These values are visualized as colored halos around the nodes, allowing overlay of protein-level measurements on the network. Example: PTEN 2.1 SMO -1.3 If numeric values are provided: - positive values are shown in blue - negative values are shown …

• string_ppi_enrichmentSTRING: Protein–protein interaction (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 random network of the same size. - The p-value reflects the likelihood that your observed number of interactions would occur by chance. - Report the p-value as a human-readable value (e.g. 2.3e-5 or 0.023). When calling related tools use the same input parameters unless otherwise specified. Outpu…

• string_proteins_for_termSTRING: Retrieve proteins associated with a functional 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 search or ask user to provide the selection. The results reflect annotation depth within each category; use caution when interpreting. If no results are found, try simplifying the query. For tissue queries, follow BRENDA tissue nomenclature and omit the word "tissue" (e.g. use "skin" instea…

• string_query_speciesSTRING: Query species and clades in STRING

  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 scientific names. - Accepts up to 100 taxon IDs separated by `%0d`. - The results are limited to the top 50 matches per query. - When the user asks for a species list, do not list clades. - If the requested species cannot be matched (i.e. the correct species is not present in the results), **immedia…

• string_resolve_proteinsSTRING: Resolves protein identifiers to metadata

  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"

Signals

Stars

7

Forks

5

Open issues

0

Last commit

Oct 2, 2026 (28 days ago)

Last release

Oct 1, 2026 (29 days ago)

From GitHub (fetched Oct 24, 2026).

Details

Registry name

org.string-db/string-mcp

Version

1.0.0

Auth

Auth not stated

License

MIT

Repository

github.com/meringlab/string-mcp

Website

mcp.string-db.org/

First seen

Oct 24, 2026

Last checked

Oct 24, 2026

Source

Official MCP Registrygithub-graphql