Uniprot MCP, developed by Smaniches, is a server tool built with Python 3.10 or higher. Distributed via PyPI as "uniprot-mcp," it serves as an MCP server for Developer Tools and AI & Agents, specifically within bioinformatics and biomedical research. It enables LLM agents, developers, and researchers to interact with the UniProtKB protein database. The tool is designed for querying protein entries, sequences, and annotations, supporting both local development and remote deployments.

What does Uniprot MCP connect to?

The Uniprot MCP server tool connects directly to the UniProtKB protein database, utilizing its public REST API for data retrieval. It functions as an MCP server, categorized under "Developer Tools" and "AI & Agents." Its primary domain is bioinformatics and biomedical research, providing a bridge for systems that need to access protein information. This allows for integration into scientific workflows and AI-driven data exploration.

Core features and tools

The uniprot-mcp package exposes several callable tools, including fetch_entry for complete protein entries, get_sequence for protein sequences, and search_uniprot for full-text search. It also provides resources like "uniprot://uniprotkb/{accession}" for raw UniProtKB JSON data and "uniprot://help/search" for search query syntax. Other implementations by different developers may offer a broader set of tools, such as map_ids or search_uniref.

Who is it for?

Uniprot MCP is designed for LLM agents, developers, and researchers active in bioinformatics, academic research, and software integration. It supports tasks requiring structured access to protein data. The tool is suitable for those needing to programmatically query protein information, generate summaries, or integrate UniProt data into larger systems. Skip this if your work requires tools like map_ids or search_uniref, which are not part of this specific implementation.

How to get started

No credentials are required as it connects to the public UniProt REST API. It supports standard input/output for local development and Streamable HTTP for remote deployments.

Use cases

• Querying protein entries, sequences, Gene Ontology annotations, and performing ID mappings.
• Fetching complete protein entries with sequences, features, GO annotations, cross-references, and taxonomy.
• Generating structured summaries of proteins, including organism, function, GO terms, and notable features.

Uniprot MCP provides a direct Python-based interface to the UniProtKB protein database, supporting vital bioinformatics and research tasks. Its design caters to LLM agents and developers needing structured access to protein data, from fetching complete entries to performing full-text searches. This implementation offers essential capabilities for integrating UniProt data. Try fetching a complete protein entry using the fetch_entry tool to explore its output.