Alphafold vs Pdbe

In-depth architectural comparison of the Alphafold and Pdbe 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?

A

Choose Alphafold when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer remote streaming HTTP/SSE transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).
• Primary tools included: prediction.

Explore Alphafold Details

Choose Pdbe when:

• You need dedicated capabilities in the Biology & Bioinformatics domain.
• You prefer remote streaming HTTP/SSE transport architecture.
• Your security boundary fits: No auth required (Free / Open Source).

Explore Pdbe Details

Feature & Specification Comparison

Specification	A Alphafold Biology & Bioinformatics	Pdbe Biology & Bioinformatics
Summary	AlphaFold DB MCP — predicted protein structures.	PDBe (Protein Data Bank in Europe, EBI) MCP.
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": {
    "alphafold": {
      "url": "https://alphafold.ebi.ac.uk/"
    }
  }
}

{
  "mcpServers": {
    "pdbe": {
      "url": "https://pipeworx.io"
    }
  }
}

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