pdb mcp for Gemini CLI

io.github.mrfentmen/pdb-mcp

RCSB PDB: search 230k+ structures, read chains, ligands, formulas and citations — keyless.

client:Gemini CLI transport:stdio runtime:npm

Install pdb mcp in Gemini CLI

~/.gemini/settings.json · windows: %USERPROFILE%\.gemini\settings.json

{
  "mcpServers": {
    "pdb-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "pdb-mcp"
      ]
    }
  }
}

Gemini expands $VAR and ${VAR} inside env values, so a secret can live in your shell rather than this file. Gemini CLI docs