Interpro vs Protein Atlas

In-depth architectural comparison of the Interpro and Protein Atlas MCP servers. Compare execution transports, security boundaries, tool capabilities, quality scores, and ready-to-paste client installation snippets for Claude, Cursor, Windsurf, and VS Code.

Which MCP Server Should You Choose?

Choose Interpro when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: search_entries, get_entry, entries_for_protein.

Explore Interpro Details

Choose Protein Atlas when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer local stdio subprocess transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: search_genes, get_protein, top_tissues.

Explore Protein Atlas Details

Feature & Specification Comparison

Specification	Interpro Biology & Bioinformatics	Protein Atlas Biology & Bioinformatics
Summary	InterPro MCP (EBI) — protein family / domain / functional-site classification.	Human Protein Atlas (HPA) MCP — keyless.
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics
Quality signal

Tools & Capabilities Breakdown

Ready-to-Paste Client Configurations

Paste either (or both) of these JSON server blocks into your client config file (e.g. claude_desktop_config.json or ~/.cursor/mcp.json).

{
  "mcpServers": {
    "interpro": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-interpro"
      ]
    }
  }
}

{
  "mcpServers": {
    "protein-atlas": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-protein-atlas"
      ]
    }
  }
}

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