Access and Query UniProt & EBI Protein Data
UniProt MCP Server provides unified access to UniProtKB and EBI Proteins API for protein data, with advanced caching.
Why it matters
Gain unified access to comprehensive protein sequence, functional, and structural data from UniProtKB and EBI Proteins API. This asset enables advanced querying, bulk loading, and analysis of protein information with intelligent caching.
Outcomes
What it gets done
Perform advanced searches and retrieve individual protein entries.
Bulk load and cache large protein datasets for efficient querying.
Map protein IDs across different databases and perform BLAST searches.
Analyze cached protein data using SQL and access detailed annotations.
Install
Add it to your toolbox
Run in your project directory:
curl -fsSL https://spark.entire.vc/get/vb-uniprot | bash Capabilities
Tools your agent gets
Advanced search across UniProtKB with comprehensive filtering and pagination
Bulk loading tool for large datasets with automatic caching
Retrieve individual UniProtKB entries by accession number
Map IDs across different database systems
Perform BLAST searches against UniProtKB
Detailed protein information from EBI Proteins API
Protein sequence features and annotations
Protein sequence variations and disease variants
Overview
UniProt MCP Server
What it does
Revised to remove unsupported claims about accelerating biological research and applications.
Source README
A comprehensive MCP server providing unified access to UniProtKB and EBI Proteins API for working with protein sequence data, functional annotations, and structural information with advanced caching capabilities.
Installation
NPM Install
npm install
Development
npm run dev
Deploy to Cloudflare
npm run deploy
MCP Remote Proxy
npx mcp-remote http://localhost:8787/sse
Configuration
Claude Desktop
{
"mcpServers": {
"uniprot": {
"command": "npx",
"args": [
"mcp-remote",
"http://localhost:8787/sse"
]
}
}
}
Available Tools
| Tool | Description |
|---|---|
uniprot_search |
Advanced search across UniProtKB with comprehensive filtering and pagination |
uniprot_stream |
Bulk loading tool for large datasets with automatic caching |
uniprot_entry |
Retrieve individual UniProtKB entries by accession number |
uniprot_id_mapping |
Map IDs across different database systems |
uniprot_blast |
Perform BLAST searches against UniProtKB |
proteins_api_details |
Detailed protein information from EBI Proteins API |
proteins_api_features |
Protein sequence features and annotations |
proteins_api_variation |
Protein sequence variations and disease variants |
proteins_api_proteomics |
Proteomics data from various studies |
proteins_api_genome |
Genome coordinate mappings |
data_manager |
Query, analyze, and manage cached datasets |
Features
- Unified interface for UniProt and EBI Proteins API
- Advanced caching with SQLite for complex queries
- Smart query generation with automatic suggestions
- Intelligent pagination for small datasets
- Scalable architecture based on Cloudflare Workers
- API rate limiting handling
- Support for multiple data formats (JSON, TSV, FASTA, XML)
- Automatic table creation and data normalization
- Bulk ID mapping across database systems
- BLAST search capabilities
Usage Examples
Search for human proteins: organism_id:9606 AND reviewed:true
Get protein details for accession P04637
Stage and query multiple proteins with SQL
Find cancer-related proteins and analyze with keywords
Search protein kinase family members
Notes
Built on Cloudflare Workers with Durable Objects for scalability. No API keys required as both UniProt and EBI Proteins API are open access. Server endpoints are available at /mcp and /sse. Includes comprehensive SQL query capabilities for analyzing cached data.
Discussion
Questions & comments · 0
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