Name: STRING Database
Author: string-db

STRING Database MCP

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

Tool-list grade A Remote · Streamable HTTP No auth needed 17 tools v1.0.0

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93/100

tool-list score

tools declared

remote

at its publisher

—

calls last 7d

What it does

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

Quickstart

# 1 — add it to Claude Code
claude mcp add --scope user --transport http string-database-mcp https://mcp.string-db.org/

# 2 — ask your agent for something these tools do
#   string_resolve_proteins, string_interactions_query_set, string_all_interaction_partners and 14 more

STRING Database costs nothing on mcprush: there is no plan to choose here, no cap to set and nothing mcprush can bill you for.

Publishernot claimed

string-db1 server

1 category

All 1 server

Collected from a public index. Nobody has claimed this account, so nothing here was written by its author — claim it if it is yours.

Tool surface

What the model actually sees. Descriptions are diffed on every release — see version history.

Only tools that write or reach the network

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"

Parameter	Type	Required	Notes
proteins	string	yes	One or more input protein identifiers (gene symbols, UniProt IDs, etc.), separated by carriage return (%0d).
species	string	no	NCBI taxonomy ID (e.g. 9606 for human) or STRING genome ID (e.g. STRG0AXXXXX for uploaded genomes).
show_sequence		no	Include sequences. Use only if the user requests sequence data.

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 be

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein identifiers, separated by carriage return (%0d).
species	string	no	NCBI taxonomy ID (e.g. 9606 for human) or STRING genome ID (e.g. STRG0AXXXXX for uploaded genomes).
required_score		no	Minimum confidence score for an interaction. Omit unless a confidence threshold is requested or a broader/narrower threshold is needed.
network_type		no	Omit for the default functional network. Its typed view can include physical and directed regulatory attributes when STRING returns them; inspect physical and regulatory.directions before claiming
network_flavor		no	Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes
extend_network		no	Number of additional proteins to add to the network based on their connectivity. Default is 10 for a single protein query and 0 for multiple proteins. Set only if the user asks to add, extend, include

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

Parameter	Type	Required	Notes
identifiers	string	yes	One or more protein identifiers, separated by carriage return (%0d).
species	string	no	NCBI taxonomy ID (e.g. 9606 for human) or STRING genome ID (e.g. STRG0AXXXXX for uploaded genomes). Only set when required.
required_score		no	Minimum interaction score to include. Omit unless a confidence threshold is requested or a broader/narrower threshold is needed.
network_type		no	Omit for the default functional network. Its typed view can include physical and directed regulatory attributes when STRING returns them; inspect physical and regulatory.directions before claiming
network_flavor		no	Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes

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 protein, such as fold change, effect size, or score. These values are visualized as colored halos arou

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein IDs, optionally followed by one numeric value per protein. Use newline (%0d) between entries. Tabs and spaces are accepted as separators.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).
extend_network		no	Add specified number of nodes to the network, based on their scores. Default: 0, or 10 for single protein queries.
required_score		no	Threshold of significance to include an interaction. Omit for STRING default filtering. Set only when a threshold is requested or a broader/narrower threshold is needed.
network_type		no	Omit for the default functional network. Its typed view can include physical and directed regulatory attributes when STRING returns them; inspect physical and regulatory.directions before claiming
network_flavor		no	Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes
hide_disconnected_nodes		no	Hide proteins not connected to any other protein. Set only if the user asks to hide disconnected or unconnected proteins.
center_node_labels		no	Center protein names on nodes. Set only if the user asks to center labels.
do_not_show_structures		no	Remove small protein structure previews from inside the node bubbles. Set only if the user asks to remove or hide structure previews.

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 consi

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein identifiers (optionally with values). Separate entries with newline (%0d). Numeric values (e.g. expression data) can be provided after identifiers.
species	string	no	NCBI/STRING taxonomy ID (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).
extend_network		no	Add specified number of additional nodes to the network based on their interaction scores. Default: 0, or 10 for single-protein queries.
required_score		no	Minimum interaction confidence score. Omit for STRING default filtering. Set only when a threshold is requested or a broader/narrower threshold is needed.
network_type		no	Omit for the default functional network. Its typed view can include physical and directed regulatory attributes when STRING returns them; inspect physical and regulatory.directions before claiming
clustering_algorithm		no	Leiden identifies natural communities based on network connectivity and is the default. MCL identifies densely connected subnetworks based on connectivity flow. kmeans partitions proteins into a fixed
clustering_parameter		no	Controls clustering granularity. For Leiden: resolution parameter 0.1-10.0, default 1.0; higher values produce more, smaller clusters. For MCL: inflation parameter 1.0-10.0, default 3.0. For kmeans: n
inter_cluster_edge_visibility		no	How to display edges between clusters: faded, dotted, solid, or noshow. Defaults to faded.
network_flavor		no	Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes
hide_disconnected_nodes		no	Hide unconnected nodes. Set only if the user asks to hide disconnected or unconnected proteins.
center_node_labels		no	Center protein labels on nodes. Set only if the user asks to center labels.

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

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein IDs, optionally followed by one numeric value per protein. Use newline (%0d) between entries. Tabs and spaces are accepted as separators.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).
extend_network		no	Add white nodes to network, based on scores. Default: 0.
required_score		no	Threshold of significance to include an interaction. Omit for STRING default filtering. Set only when a threshold is requested or a broader/narrower threshold is needed.
network_flavor		no	Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes
network_type		no	Omit for the default functional network. Its typed view can include physical and directed regulatory attributes when STRING returns them; inspect physical and regulatory.directions before claiming
hide_disconnected_nodes		no	Hide proteins not connected to any other protein. Set only if the user asks to hide disconnected or unconnected proteins.

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

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein identifiers, separated by %0d.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).
species_b		no	One or more NCBI taxon IDs for target species, separated by comma (e.g. 9606,7227,4932 for human, fly, and yeast).

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) suppor

Parameter	Type	Required	Notes
identifier_a	string	yes	Protein A identifier.
identifiers_b	string	yes	One or more protein B identifiers, separated by %0d.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).
network_type		no	Set physical for physical-interaction evidence or regulatory for directed regulatory evidence. Omit for the functional interaction evidence page.

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

Parameter	Type	Required	Notes
proteins	string	yes	One or more protein identifiers, separated by %0d.
species		no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX). Use only when required.
expand_category		no	Return only this enrichment category with expanded term coverage and a larger per-term gene-list cutoff. Use a category from metadata.category_summary.

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 s

Parameter	Type	Required	Notes
identifiers	string	yes	Separate multiple protein queries by %0d.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).
detail_for_term		no	Exact functional term ID to return with the full list of matching input proteins. Use this when a previous result says a protein list was shortened, omitted, or replaced with 'many'.

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.

Parameter	Type	Required	Notes
identifiers	string	yes	Protein identifiers, separated by %0d.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).
category		no	Term category for enrichment. If omitted, STRING uses Process. Use Process/Function/Component for GO, KEGG for KEGG pathways, RCTM for Reactome, and PMID for publications.
group_by_similarity		no	Visually groups terms based on term similarity. Default: 0.8. Details: string_help topic 'enrichment_grouping'.
color_palette		no	Color palette for FDR. If omitted, STRING uses mint_blue.
number_of_terms_shown		no	Max number of terms shown on plot. Default: 10.
x_axis		no	Value shown on the X-axis; also selects and orders the terms. If omitted, STRING uses signal.
graph_type		no	Plot type: dotplot or barplot (horizontal bar chart). If omitted, STRING uses dotplot.

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

Parameter	Type	Required	Notes
identifiers	string	yes	One or more protein identifiers, separated by %0d.
species	string	no	NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).
required_score		no	Minimum interaction confidence score. Omit unless a confidence threshold is requested or a broader/narrower threshold is needed.

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 ca

Parameter	Type	Required	Notes
term_text	string	yes	Functional term identifier (GO, KEGG, Reactome, etc.) or descriptive free text.
species	string	no	NCBI/STRING taxonomy ID. This tool only supports one species per call. It cannot return results across multiple species or identify the species with the most/fewest proteins. For such questions, run t
detail_for_term		no	Exact term ID to return as one full protein-name list.

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.

Parameter	Type	Required	Notes
sequences	string	yes	One or more protein sequences in plain or FASTA format.For multiple sequences, use standard FASTA headers (lines beginning with '>'). Only amino acid sequences are supported — nucleotide sequences are
species	string	no	NCBI or STRING taxonomy ID. You can query with a clade or species. eg.g 2 for bacteria, 7742 for vertebrates, 511145 for E. coli

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 t

Parameter	Type	Required	Notes
species_text	string	yes	One species/clade search term or multiple NCBI taxon IDs separated by carriage return (%0d). For multiple queries, use taxon IDs rather than free-text names.

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 downloa

Parameter	Type	Required	Notes
filename	string	yes	Suggested output filename with a safe extension such as .tsv, .csv, .json, .md, or .txt. Match content to the extension; prefer .tsv for reusable tabular STRING data. Use a concise name that reflects
content	string	yes	STRING-derived file content. For .tsv/.csv: one rectangular table, one header row, matching delimiter, no Markdown/prose/repeated headers/multiple tables. Use one row per entity, edge, cluster member,

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 (enric

Parameter	Type	Required	Notes
topic		no	Help topic to display. If omitted, returns the available topics.

Free

$0 forever

Every tool — any call limit is its publisher’s, not ours
No card, and mcprush charges nothing for it
Runs at its publisher’s own address — this marketplace is not in the path
Nothing to cap, because mcprush bills nothing

Nothing here is billable: mcprush charges nothing to install STRING Database or to call it, at any volume.

ATool-list grade · score 93 / 100

Release 1.0.0 · scanned 20 Oct 2026

Graded from the tools this server lists, not from its source code.

Two independent axes, because powerful and malicious are different questions. The grade is threat only. The capability level is blast radius, and it is never a penalty on the grade — it is priced as one subtract-only term in the score, where you can see it.

Threat score100

Client score93

Findings0 threat · 3 capability

Capabilitymoderate

Coveragemanifest

Verificationnot in this report

Surface digestef0f3abb507574f64135666e570b80e06d409b59ac797777c56b786c4d21c09c

Score vectorthreat 100 → client 93

Term	Level	What it prices	Points
capability-exposure	moderate	capability blast radius (moderate) — client exposure if the model is manipulated	−3
coverage-honesty	manifest	inspection depth (manifest) — how much of the target the scan could see	−4

score = clamp(round(threatScore − E_cap − E_ver − E_cov), 0, 100). No model, no opinion, no network call at scoring time: the same methodology version against the same bytes always produces this number, and every line above is a field of the report rather than a summary of it.

What the scan could actually read

A grade is only as meaningful as its coverage, so the scanner publishes its own depth before it publishes its result.

The scan read each tool’s name, description, input schema and annotations exactly as the server listed them the last time it answered us; no code was reviewed. We ask the server again about once a month, and a list that changed is graded again.

Tool surfaceread

Implementation sourcenot available

Package metadatanot available

Live transportnot available

The implementation source was not read — this reflects the declared tool metadata only.

Capability — what it could do if the model were manipulated

Tags derived from each tool’s schema and the implementation, not from what the tool calls itself. moderate is the level these add up to.

Tool	Capability tags	Why the tag was assigned
string_resolve_proteins	no tags
string_interactions_query_set	no tags
string_all_interaction_partners	no tags
string_visual_network	no tags
string_network_clustering	no tags
string_network_link	no tags
string_homology	no tags
string_interaction_evidence	no tags
string_enrichment	no tags
string_functional_annotation	no tags
string_enrichment_image_url	no tags
string_ppi_enrichment	no tags
string_proteins_for_term	no tags
string_sequence_search	no tags
string_query_species	no tags
string_create_file	file-write	file-write: keyword "create_file" in tool name
string_help	no tags

Toxic-flow graph

The lethal trifecta, checked as a graph rather than as a checklist: untrusted input, a sensitive source and an external sink have to meet before there is a path worth worrying about.

The public result for this release does not print the flow graph, so there is nothing to show here. That is not the same as "no paths were found": what the scan did read is above, under coverage.

Supply chain and provenance

Integrityfirst-seen

Surface digestef0f3abb507574f6

Scanned2026-10-20

This is the first scan of this surface here, so there is nothing yet to compare it against.

Every result on this tab comes from one deterministic pass over the published package — offline, rule by rule, and auditable line by line above. Same methodology version, same bytes, same score.

Where are you running it?

Tool surface

Release history

STRING Database MCP

What it does

Quickstart

Where are you running it?

Tool surface

What counts against your monthly calls

What the scan could actually read

Capability — what it could do if the model were manipulated

Toxic-flow graph

Supply chain and provenance

Release history

See also