AlphaFold Sovereign

About

Wraps AlphaFold DB, MONDO, HPO, Open Targets, ClinVar, gnomAD, DisGeNET, ChEMBL and Ensembl behind MCP tool calls. It also combines them into multi-source workflows such as variant cross-reference reports, disease-target summaries, heuristic druggability scoring, drug-repurposing ranking and structural-distance comparison using persistent-homology fingerprints. A local SQLite knowledge graph offers query, export and traversal tools.

Runs as a local Python process over stdio, started with uvx alphafold-sovereign-mcp (Python 3.10 to 3.13). In online mode the tools send identifiers to the public upstream APIs, and DisGeNET needs its own free API key. Setting ALPHAFOLD_OFFLINE=1 blocks outbound requests. Outputs are research aids, not for clinical use without expert review.

What you can do

• Fetch AlphaFold DB protein structure data
• Query ClinVar, gnomAD, Ensembl, ChEMBL and Open Targets
• Look up disease and phenotype terms in MONDO and HPO
• Generate draft variant cross-reference reports
• Score target druggability with a heuristic tier
• Compare proteins by topological structural distance
• Query and export a local SQLite knowledge graph
• Run offline so no identifiers leave the machine

Tools

Local servers list their tools once they’re running, so we can’t show them here. Look for the list in its documentation; your client shows them after you add it.

Example prompts

• Fetch the AlphaFold structure for human TP53 and summarize its pLDDT confidence

• Build a variant cross-reference report for BRCA1 c.5266dupC

• Assess the druggability of EGFR using Open Targets and ChEMBL data

• Show the diseases linked to a target in the local knowledge graph

Set up

Every client starts AlphaFold Sovereign on your machine with the same command. Pick yours; the page remembers your choice.

claude mcp add --transport stdio alphafold-sovereign -- uvx alphafold-sovereign-mcp

{
  "mcpServers": {
    "alphafold-sovereign": {
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

{
  "mcpServers": {
    "alphafold-sovereign": {
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

code --add-mcp '{"name":"alphafold-sovereign","type":"stdio","command":"uvx","args":["alphafold-sovereign-mcp"]}'

{
  "servers": {
    "alphafold-sovereign": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

{
  "mcpServers": {
    "alphafold-sovereign": {
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

codex mcp add alphafold-sovereign -- uvx alphafold-sovereign-mcp

[mcp_servers.alphafold-sovereign]
command = "uvx"
args = ["alphafold-sovereign-mcp"]

gemini mcp add alphafold-sovereign uvx alphafold-sovereign-mcp

{
  "mcpServers": {
    "alphafold-sovereign": {
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

Embed

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README badge

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iframe

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JSON

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https://mcp.tc/i/alphafold-sovereign.json

What each field means

AI prompt

Paste this into an AI coding assistant, such as Claude Code or Cursor, and it adds the AlphaFold Sovereign card to your site.

Markdown

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Put this tag where the card should appear. The card renders right before it:

```html
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```

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```html
<div data-mcptc="alphafold-sovereign"><a href="https://mcp.tc/i/alphafold-sovereign">AlphaFold Sovereign on mcp.tc</a></div>
```

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```markdown
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```

Reference: https://mcp.tc/embed

Change history

This server runs on your computer, so we follow its PyPI package: each new version shows up here, with edits by its owner.

1. 6 Oct 2026, 21:21 UTC, Automatic check

   Tracking started: version 1.4.10.

FAQ