Pdbe vs Uniprot MCP Server

In-depth architectural comparison of the Pdbe and Uniprot MCP Server 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 Pdbe 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).

Explore Pdbe Details

Choose Uniprot MCP Server 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).

Explore Uniprot MCP Server Details

Feature & Specification Comparison

Specification	Pdbe Biology & Bioinformatics	Uniprot MCP Server Biology & Bioinformatics
Summary	PDBe (Protein Data Bank in Europe, EBI) MCP.	Protein research over UniProtKB — search by function, fetch curated records, map IDs, proteomes.
Category & Scope	Biology & Bioinformatics	Biology & Bioinformatics

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": {
    "pdbe": {
      "command": "npx",
      "args": [
        "-y",
        "pdbe"
      ]
    }
  }
}

{
  "mcpServers": {
    "uniprot-mcp-server": {
      "command": "bunx",
      "args": [
        "@cyanheads/uniprot-mcp-server@latest"
      ]
    }
  }
}

Related MCP Server Comparisons