Koskamo

PDBe MCP

The PDBe MCP server provides three keyless tools to query the Protein Data Bank in Europe (EBI). It allows agents to retrieve PDB entry summaries, list molecules and entities within structures, and access SIFTS cross-database mappings to UniProt. This enables biological data analysis without authentication overhead.

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Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

PDBe MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Retrieve PDB entry summaries including experimental method and release date
  • List proteins, nucleic acids, and ligands in a PDB structure
  • Access SIFTS cross-database mappings of PDB structures to UniProt

Source and maintenance

Community listingRegistry 0.2.0
mcp-registry: io.github.pipeworx-io/pdbe@0.2.0Source repositoryProject website
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-pdbe 0.2.0

npm
@pipeworx/mcp-pdbe package definition
{
  "version": "0.2.0",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-pdbe",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "pdbe-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pdbe@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "pdbe-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pdbe@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "pdbe-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pdbe@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "pdbe-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-pdbe@0.2.0"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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