# AlphaFold Sovereign MCP server

> Query AlphaFold DB and eight other biomedical sources from one local server with a SQLite knowledge graph.

- Listing: https://mcp.tc/i/alphafold-sovereign
- Connect: this is a local (stdio) server; install it on your machine (see Install). The listing link is a page, not an MCP endpoint.
- Type: local (stdio)
- Auth: no API key needed
- Category: [AI & Machine Learning](https://mcp.tc/c/ai-ml)
- Vendor: smaniches
- Homepage: <https://topologica.ai>
- Docs: <https://smaniches.github.io/alphafold-sovereign-mcp/>
- Repository: <https://github.com/smaniches/alphafold-sovereign-mcp>
- Package: pypi `alphafold-sovereign-mcp`

## 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 it 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

## 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"

## Install

### Claude Code

1. Run this in a terminal, in your project folder:

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

2. Start Claude Code and type `/mcp`. **alphafold-sovereign** should show as connected.

Add `--scope user` to make it available in every project.

### Claude Desktop

1. Open **Settings → Developer → Edit Config**. It opens `claude_desktop_config.json`. Add:

`claude_desktop_config.json`:

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

2. Save the file and restart Claude Desktop.

Needs uv (Python) on your computer. The file lives in `~/Library/Application Support/Claude/` on macOS and `%APPDATA%\Claude\` on Windows.

### Cursor

[Add to Cursor](<https://cursor.com/install-mcp?name=alphafold-sovereign&config=eyJjb21tYW5kIjoidXZ4IiwiYXJncyI6WyJhbHBoYWZvbGQtc292ZXJlaWduLW1jcCJdfQ%3D%3D>) (opens Cursor)

Or add it by hand to `~/.cursor/mcp.json` (all projects) or `.cursor/mcp.json` (this project):

`mcp.json`:

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

Needs uv (Python) on your computer.

### VS Code

[Install in VS Code](<https://vscode.dev/redirect/mcp/install?name=alphafold-sovereign&config=%7B%22type%22%3A%22stdio%22%2C%22command%22%3A%22uvx%22%2C%22args%22%3A%5B%22alphafold-sovereign-mcp%22%5D%7D>) (opens VS Code)

Or from a terminal:

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

Or commit it to the repo in `.vscode/mcp.json`:

`.vscode/mcp.json`:

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

Needs uv (Python) on your computer.

### Devin Desktop

1. Add it to `~/.config/devin/mcp_config.json` (macOS and Linux) or `%APPDATA%\devin\mcp_config.json` (Windows):

`mcp_config.json`:

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

2. Refresh the MCP server list in Cascade.

Devin Desktop is the new name for Windsurf.

### Codex

```bash
codex mcp add alphafold-sovereign -- uvx alphafold-sovereign-mcp
```

Or edit `~/.codex/config.toml` directly:

`config.toml`:

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

Needs uv (Python) on your computer.

### Gemini CLI

```bash
gemini mcp add alphafold-sovereign uvx alphafold-sovereign-mcp
```

This adds it to the current project. Add `-s user` to use it everywhere.

### Any client

Most clients that start local servers accept this shape:

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

Zed puts servers under `context_servers` in its settings, with the same `command`, `args` and `env` fields.

Needs uv (Python) on your computer.

## Recent changes

- 2026-10-06 21:21 UTC: Tracking started: version 1.4.10. Source: automatic check.

More on the History tab, with descriptions before and after for the newest entries: https://mcp.tc/i/alphafold-sovereign#history (Atom feed: https://mcp.tc/i/alphafold-sovereign/history.xml). It records what mcp.tc's anonymous checks saw, every 3 hours where the tool list can be read without sign-in; it is not a security review.

## Details

- Server version: 1.4.10
- Last checked: 2026-10-05
- Listed: 2026-10-05
- Updated: 2026-10-05

---
Source: https://mcp.tc/i/alphafold-sovereign (mcp.tc is an independent directory, not affiliated with this server's publisher). Corrections: https://mcp.tc/report