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query_alphafold

skillby Eijex
StructureAlphaFoldBiotech

Queries the AlphaFold Protein Structure Database (EBI) for a predicted 3D structure. Returns model version, organism, coverage, and direct download links for PDB, CIF, and PAE files. Use query_uniprot first to find the UniProt accession.

Key Features

1.

AlphaFold EBI API — no API key required

2.

Returns PDB, CIF, and PAE download links

3.

Includes model version and organism coverage

Use Cases

  1. 1.Fetching predicted 3D structure for a target protein
  2. 2.Downloading PAE data for domain boundary analysis
  3. 3.Checking AlphaFold model coverage before wet-lab design

Parameters

NameTypeRequiredDescription
uniprot_accessionstringrequiredUniProt accession (e.g. "P42212"). Use query_uniprot to find it.

Connection

.mcp.json / Claude Code settingsJSON
{
  "mcpServers": {
    "eijex": {
      "type": "http",
      "url": "https://mcp.eijex.com/api/mcp"
    }
  }
}

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