Unofficial STRING MCP Server
A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.
Features
Tools (6 comprehensive tools)
get_protein_interactions: Get direct interaction partners for a specific protein with confidence scores and evidence types
get_interaction_network: Build and analyze protein interaction networks for multiple proteins
get_functional_enrichment: Perform functional enrichment analysis using GO terms, KEGG pathways, and other annotations
get_protein_annotations: Get detailed protein annotations and functional information
find_homologs: Find homologous proteins across different species for comparative analysis
search_proteins: Search for proteins by name or identifier across multiple species
Resources (6 resource templates)
string://network/{protein_ids}: Protein interaction network data for specified proteins
string://enrichment/{protein_ids}: Functional enrichment analysis results for protein sets
string://interactions/{protein_id}: Direct interaction partners for a specific protein
string://homologs/{protein_id}: Homologous proteins across different species
string://annotations/{protein_id}: Detailed protein annotations and functional information
string://species/{taxon_id}: Species-specific data and protein counts
Installation
Usage
With Claude Desktop
Add to your claude_desktop_config.json
:
Example Queries
Find protein interactions:
Get interaction partners for insulin (INS) using get_protein_interactionsBuild protein networks:
Build an interaction network for insulin signaling proteins: INS, INSR, IRS1, AKT1 using get_interaction_networkFunctional enrichment analysis:
Perform functional enrichment analysis on these diabetes-related proteins: INS, INSR, IRS1, GLUT4, AKT1Find protein homologs:
Find homologs of human insulin (INS) in mouse and rat using find_homologsSearch for proteins:
Search for insulin-related proteins using search_proteins with query "insulin"Get protein annotations:
Get detailed annotations for insulin receptor pathway proteins using get_protein_annotationsAccess resources directly:
Show me the resource string://network/INS,INSR,IRS1
API Integration
This server integrates with the STRING Database API (https://string-db.org/):
STRING REST API: For protein interaction data, annotations, and homology information
Multi-species support: Over 5000 organisms supported
Evidence types: Neighborhood, fusion, cooccurrence, coexpression, experimental, database, textmining
Confidence scoring: Interaction confidence scores from 0-1000
Key Features
Protein Interaction Analysis
Direct interactions: Find immediate interaction partners
Network construction: Build comprehensive interaction networks
Evidence classification: 7 types of interaction evidence
Confidence scoring: Quantitative interaction confidence
Functional Analysis
GO enrichment: Gene Ontology term enrichment
KEGG pathways: Metabolic and signaling pathway analysis
Custom backgrounds: Use custom protein sets as background
Statistical significance: P-values and FDR correction
Comparative Genomics
Cross-species analysis: Find homologs across organisms
Evolutionary relationships: Analyze protein evolution
Species filtering: Focus on specific taxonomic groups
Ortholog identification: Distinguish orthologs from paralogs
Network Properties
Topology analysis: Network density, clustering, connectivity
Hub identification: Find highly connected proteins
Module detection: Identify protein complexes and modules
Path analysis: Find shortest paths between proteins
Complementary Servers
This STRING server works excellently with:
UniProt MCP Server: For protein sequences and detailed functional annotations
PDB MCP Server: For protein structures and structural analysis
AlphaFold MCP Server: For predicted protein structures
Together, these provide comprehensive protein analysis: Sequence → Structure → Interactions → Function
Data Quality & Validation
Curated data: STRING combines curated databases with computational predictions
Evidence integration: Multiple evidence types combined using probabilistic framework
Regular updates: Database updated regularly with new experimental data
Quality scores: Each interaction has associated confidence scores
Error Handling
The server includes robust error handling for:
Invalid protein identifiers
Network connectivity issues
API rate limiting
Species validation
Parameter validation
Malformed requests
Development
Attribution
This project is developed by Augmented Nature 🌐 Website: augmentednature.ai
About STRING Database: STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.
Citation
If you use this project in your research or publications, please cite it as follows:
remote-capable server
The server can be hosted and run remotely because it primarily relies on remote services or has no dependency on the local environment.
Tools
A comprehensive Model Context Protocol (MCP) server for accessing the STRING protein interaction database. This server provides powerful tools for protein network analysis, functional enrichment, and comparative genomics through the STRING API.
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