STRING Database

listing.about

Connects an assistant to the STRING database of protein-protein interactions. You can resolve protein identifiers, list interaction partners, build and cluster networks, run functional and PPI enrichment, fetch curated annotations, find homologs across species and get links to interaction evidence pages.

It runs as a hosted streamable HTTP endpoint at mcp.string-db.org, and no sign-in or API key is needed. The source is MIT licensed and can also be run locally with Python 3.11 or newer, over HTTP or stdio, or in Docker.

listing.can

• Resolve gene and protein names to STRING IDs and metadata
• List interaction partners and interactions within a protein set
• Generate network images and interactive STRING network links
• Cluster interaction networks and describe each cluster
• Run functional enrichment and PPI enrichment tests
• Retrieve GO, KEGG and other functional annotations
• Find homologs and search proteins by amino acid sequence
• Export results as downloadable files

listing.tools 17

• string_resolve_proteins

  Map protein identifiers to STRING metadata such as gene symbol, species and STRING ID.

• string_interactions_query_set

  Get interactions between the proteins in the query set.

• string_all_interaction_partners

  Get all interaction partners of the query proteins across STRING.

• string_visual_network

  Get a URL to a STRING network image, optionally with per-protein values.

• string_network_clustering

  Cluster a STRING network and return images, links and cluster details.

• string_network_link

  Get a stable URL to an interactive STRING network.

• string_homology

  Get pairwise homology bit scores within or across species.

• string_interaction_evidence

  Get links to STRING evidence pages for protein pairs.

• string_enrichment

  Run functional enrichment analysis on a protein set.

• string_functional_annotation

  Retrieve curated annotations such as GO, KEGG and UniProt keywords.

• string_enrichment_image_url

  Get an enrichment figure URL for a chosen category.

• string_ppi_enrichment

  Test whether a network has more interactions than expected by chance.

listing.prov.live_on

listing.prompts

• What does TP53 interact with in human? Show only high-confidence partners.

• Run functional enrichment on BRCA1, BRCA2, ATM and CHEK2.

• Cluster the network for these proteins and describe each cluster.

• Find yeast homologs of human SMO and give the taxon IDs.

listing.setup.h

listing.setup.remote

claude mcp add --transport http string-db https://mcp.string-db.org/

https://mcp.string-db.org/

{
  "mcpServers": {
    "string-db": {
      "url": "https://mcp.string-db.org/"
    }
  }
}

code --add-mcp '{"name":"string-db","type":"http","url":"https://mcp.string-db.org/"}'

{
  "servers": {
    "string-db": {
      "type": "http",
      "url": "https://mcp.string-db.org/"
    }
  }
}

{
  "mcpServers": {
    "string-db": {
      "serverUrl": "https://mcp.string-db.org/"
    }
  }
}

codex mcp add string-db --url https://mcp.string-db.org/

[mcp_servers.string-db]
url = "https://mcp.string-db.org/"

gemini mcp add --transport http string-db https://mcp.string-db.org/

{
  "mcpServers": {
    "string-db": {
      "type": "http",
      "url": "https://mcp.string-db.org/"
    }
  }
}

listing.faq

listing.em.h

listing.em.lead listing.em.how

listing.em.badge listing.em.widget iframe JSON

listing.em.badge

Markdown

[![STRING Database on mcp.tc](https://mcp.tc/i/string-db/badge.svg)](https://mcp.tc/i/string-db)

HTML

<a href="https://mcp.tc/i/string-db"><img src="https://mcp.tc/i/string-db/badge.svg" alt="STRING Database on mcp.tc" height="20"></a>

listing.em.badge_note

listing.em.widget

HTML

<script src="https://mcp.tc/w/string-db.js" async></script>

listing.em.widget_note

iframe

HTML

<iframe src="https://mcp.tc/embed/string-db" title="STRING Database on mcp.tc" width="420" height="200" loading="lazy" allow="clipboard-write" style="border:0;border-radius:8px;max-width:100%"></iframe>

listing.em.iframe_note

JSON

listing.em.json

https://mcp.tc/i/string-db.json

listing.em.fields