STRING is a database of known and predicted protein-protein interactions and a functional enrichment tool.
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Explore capabilities (17)
other 17
String
17
STRING: Resolves protein identifiers to metadata
other
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: 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"
STRING: 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.
If user asks for 'physical' or 'complex' use 'physical' network type.
- 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.
- If the user refe
STRING: 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 the `network` tool, which only shows interactions **within the input set** or a limited extension of it.
- If the user refers to "physical interactions", "complexes", or "binding", set the network type to "physical".
You can
STRING: Get interaction network image (image URL) — 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**.
- If the user asks for "physical interactions", "complexes", or "binding", set `network_type` to "physical".
The input may include one numeric value per protein, such as fold change, effect size, or score.
These values are visualized as colored h
STRING: Perform 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 network already contains disconnected subgraphs, the resulting number of clusters may differ from the requested value.
Dashed lines represent connections between clusters, while solid lines indicate interactions within clusters.
Notes:
- For small queries (≤5 pro
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What is the STRING: functional protein association networks MCP server?
STRING is a database of known and predicted protein-protein interactions and a functional enrichment tool.
How do I connect STRING: functional protein association networks to my AI agent?
Use the MCP endpoint listed on this page in your MCP client configuration. One-click install pills support Claude, Cursor, VS Code, and other hosts. Copy the remote MCP URL if your client needs a manual entry.
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STRING: 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**.
- If the user asks for "physical interactions", "complexes", or "binding", set `network_type` to "physical".
The input may include one numeric value per protein, such as fold change, effect size, or score.
These values are visualized as colored hal
STRING: 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 <
STRING: 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
STRING: 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
STRING: 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 too
STRING: Get enrichment result figure (image URL) — Retrieves the STRING enrichment figure image *URL* for a set of proteins.
STRING: 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
STRING: 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 ti
STRING: Search proteins by amino acid sequence — 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 is unknown or unresolvable by `string_resolve_proteins`.
STRING: 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 reque
STRING: 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
STRING: 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, regulatory networks, large datasets).
- meaning of the lines in the network (line_colors)
How many tools does STRING: functional protein association networks provide?
MCPBundles probed 17 tools on the live server. The tool list on this page reflects what was discovered at the last refresh — connect your client to see the full set available to your session.
What authentication does STRING: functional protein association networks require?
No provider sign-in was required during MCPBundles' probe. Your client may still need MCPBundles credentials depending on how you connect.
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