AlphaFold MCP Server

MCP wrapper over the EBI AlphaFold Protein Structure Database — predicted structures for any UniProt protein, with built-in confidence analysis and visualization export.


Type	MCP server
Supplier	Augmented Nature (community OSS)
Availability	GA — active, ~25 tools
Pricing	Free / OSS (MIT); EBI AlphaFold DB is free for academic use
Capabilities	Read-only

How to install

Also packaged in the SciAgent-Skills collection (jaechang-hits (community OSS, CC BY 4.0)): clone jaechang-hits/SciAgent-Skills and run /plugin install sciagent-skills in Claude Code (or copy skills/structural-biology-drug-discovery/alphafold-database-access into ~/.claude/skills/).
```
git clone https://github.com/Augmented-Nature/AlphaFold-MCP-Server
cd AlphaFold-MCP-Server
npm install
npm run build
```

Then add to claude_desktop_config.json (replace /path/to/AlphaFold-MCP-Server with the absolute path of your clone — e.g., /Users/you/repos/AlphaFold-MCP-Server):

{
  "mcpServers": {
    "alphafold-server": {
      "command": "node",
      "args": ["/path/to/AlphaFold-MCP-Server/build/index.js"]
    }
  }
}

For Claude Code, the equivalent registration is:

claude mcp add --transport stdio alphafold-server -- node /path/to/AlphaFold-MCP-Server/build/index.js

What it does

About 25 tools across:

Retrieval: get_structure, download_structure (PDB / CIF / BCIF / JSON by UniProt ID)
Confidence: get_confidence_scores, analyze_confidence_regions (pLDDT)
Batch / comparative: batch_structure_info (up to 50 proteins), compare_structures, find_similar_structures
Visualization export: export_for_pymol, export_for_chimerax

Primary use cases: Pull AlphaFold predictions by UniProt for a target list, flag low-pLDDT regions before docking or modelling, prepare PyMOL / ChimeraX sessions for analysis.

Notes

Node/stdio transport. No auth — hits https://alphafold.ebi.ac.uk/api/. Complements the PDB MCP server (experimental structures) by covering predictions.

Sources

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