ProteinAtlas MCP Server

Proteinatlas mcp server connects ProteinAtlas to AI assistants that speak the Model Context Protocol. A comprehensive Model Context Protocol server for accessing Human Protein Atlas data including tissue expression, subcellular localization, pathology data, and protein annotations.

What ProteinAtlas does

A comprehensive Model Context Protocol (MCP) server for accessing Human Protein Atlas data, providing information about protein expression, subcellular localization, pathology, and more.

The Human Protein Atlas MCP Server enables seamless access to the vast repository of protein data from the Human Protein Atlas (https://www.proteinatlas.org). This server provides tools and resources for:

Tools it exposes

Once connected, the assistant can call these 14 tools directly:

• Prerequisites — The Prerequisites tool exposed by this server
• Setup — 1. Clone or download the server code 2. Install dependencies:
• search_proteins — Search Human Protein Atlas for proteins by name, gene symbol, or description
• get_protein_info — Get detailed information for a specific protein by gene symbol
• get_protein_by_ensembl — The get_protein_by_ensembl tool exposed by this server
• get_tissue_expression — The get_tissue_expression tool exposed by this server
• search_by_tissue — The search_by_tissue tool exposed by this server
• get_blood_expression — The get_blood_expression tool exposed by this server
• get_brain_expression — The get_brain_expression tool exposed by this server
• get_subcellular_location — The get_subcellular_location tool exposed by this server
• search_by_subcellular_location — Find proteins localized to specific subcellular compartments
• get_pathology_data — The get_pathology_data tool exposed by this server
• search_cancer_markers — Find proteins associated with specific cancers or with prognostic value
• advanced_search — The advanced_search tool exposed by this server

Installing the proteinatlas mcp server

Setup follows the standard MCP pattern: clone or install the server, then register it in your client's configuration file and restart the client. The configuration snippets on this page cover Claude Desktop, Claude Code and Cursor.

Requirements

• Node.js 18 or higher - npm or yarn package manager

Where it fits

Developer-tool servers are usually the first ones people connect, because they turn "help me with this code" into an assistant that can actually read the repo and act on it. ProteinAtlas sits in that group, and the shape of its toolset — Prerequisites, Setup, search_proteins among others — tells you what it is really for. Worth comparing against the other developer tools servers in this directory before you commit to one, since several overlap in scope but differ sharply in setup cost and permissions.

Practical notes

• This server runs locally, so it operates with whatever access your machine and its credentials already have. Scope that deliberately rather than by default.
• With 14 tools exposed, expect a noticeable bump in prompt size — disable it in projects that never use ProteinAtlas.
• Maintained by Augmented-Nature, written in TypeScript.
• MCP clients ask for confirmation before each tool call by default. Keep that on while you learn what the proteinatlas mcp server actually does with your data.
• Every entry in this directory is reviewed by hand before it goes live, and details are checked against the project's own documentation.