AI Atlas

Research & Data · Developer Tools

Augmented-Nature-UniProt-MCP-Server

Augmented-Nature/Augmented-Nature-UniProt-MCP-Server

A comprehensive Model Context Protocol (MCP) server providing advanced access to the UniProt protein database.

View on GitHub

Install

docker run -i uniprot-mcp-server

Client configuration

{
  "mcpServers": {
    "uniprot": {
      "command": "docker",
      "args": [
        "run",
        "-i",
        "uniprot-mcp-server"
      ]
    }
  }
}
Author
@Augmented-Nature
Category
Research & Data, Developer Tools
License
MIT
Updated
Oct 6, 2026

About Augmented-Nature-UniProt-MCP-Server

This server offers 26 specialized bioinformatics tools enabling AI assistants and MCP clients to perform sophisticated protein research, comparative genomics, structural biology analysis, and systems biology investigations directly through UniProt's REST API.

Features

  • Protein Search: Search the UniProt database by protein name, keywords, or organism

  • Detailed Protein Info: Retrieve comprehensive protein information including function, structure, and annotations

  • Gene-based Search: Find proteins by gene name or symbol

  • Sequence Retrieval: Get amino acid sequences in FASTA or JSON format

  • Feature Analysis: Access functional domains, active sites, binding sites, and other protein features

  • Protein Comparison: Side-by-side comparison of multiple proteins with sequence and feature analysis

  • Homolog Discovery: Find homologous proteins across different species

  • Ortholog Identification: Identify orthologous proteins for evolutionary studies

  • Phylogenetic Analysis: Retrieve evolutionary relationships and phylogenetic data

  • 3D Structure Information: Access PDB references and structural data

Tools (26)

  • search_proteins

    Search the UniProt database for proteins by name, keyword, or organism.

  • get_protein_info

    Get detailed information for a specific protein by UniProt accession.

  • search_by_gene

    Search for proteins by gene name or symbol.

  • get_protein_sequence

    Get the amino acid sequence for a protein.

  • get_protein_features

    Get functional features and domains for a protein.

  • compare_proteins

    Compare multiple proteins side-by-side

  • get_protein_homologs

    Find homologous proteins across species

  • get_protein_orthologs

    Identify orthologous proteins

  • get_phylogenetic_info

    Retrieve evolutionary relationships

  • get_protein_structure

    Access 3D structure information from PDB

  • get_protein_domains_detailed

    Enhanced domain analysis (InterPro, Pfam, SMART)

  • get_protein_variants

    Disease-associated variants and mutations

  • analyze_sequence_composition

    Amino acid composition analysis

  • get_protein_pathways

    Associated biological pathways (KEGG, Reactome)

  • get_protein_interactions

    Protein-protein interaction networks

  • search_by_function

    Search by GO terms or functional annotations

  • search_by_localization

    Find proteins by subcellular localization

  • batch_protein_lookup

    Process multiple accessions efficiently

  • advanced_search

    Complex queries with multiple filters

  • search_by_taxonomy

    Search by taxonomic classification

  • get_external_references

    Links to other databases (PDB, EMBL, RefSeq, etc.)

  • get_literature_references

    Associated publications and citations

  • get_annotation_confidence

    Quality scores for annotations

  • export_protein_data

    Export in specialized formats (GFF, GenBank, EMBL, XML)

  • validate_accession

    Check accession number validity

  • get_taxonomy_info

    Detailed taxonomic information

Details on this page are taken from the project's README. Open README

Supported clients

Clients mentioned in this server's README:

View all
Claude Desktop logo

Claude Desktop

Desktop · Freemium · Proprietary

Anthropic's official Claude AI desktop application. Supports MCP servers to extend functionality.

WindowsMacOS

Related MCP servers

More servers
Firecrawl MCP Server logo

Firecrawl MCP Server

mendableai/firecrawl-mcp-server

2.8k

A Model Context Protocol (MCP) server that brings Firecrawl to MCP-compatible AI agents — search, scrape, and interact with the live web for clean, agent-ready context.

Research & Data
Exa Web Search logo

Exa Web Search

exa-labs/exa-mcp-server

1.4k

Connect AI agents to Exa for web search, content fetching, and multi-step research.

Research & Data
ArXiv logo

ArXiv

blazickjp/arxiv-mcp-server

1k

A local MCP server for agent literature work. The differentiator is original-LaTeX section reads, BibTeX from arXiv metadata, and topic watches. Papers stay on disk.

Research & Data
sail logo

sail

lakehq/sail

730

Sail is a drop-in Apache Spark replacement written in Rust, unifying batch processing, stream processing, and compute-intensive AI workloads on a distributed, multimodal compute engine.

Research & Data

OpenAPI Proxy

janwilmake/openapi-mcp-server

554

A Model Context Protocol (MCP) server for Claude/Cursor that enables searching and exploring OpenAPI specifications through oapis.org.

Research & Data
Excel MCP Server logo

Excel MCP Server

haris-musa/excel-mcp-server

393

A Model Context Protocol server that lets AI assistants create, read and edit Excel workbooks. It needs no Microsoft Excel installation.

Research & Data