AlphaFold MCP

The AlphaFold MCP server provides access to predicted 3-D protein structures for approximately 214 million sequences. It offers tools to retrieve full prediction metadata, structure file URLs (PDB, CIF, PAE), short summaries, sequence-level annotations, and UniProt-based metadata lookups.

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Package and access

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

Community listingLocal stdioSource reviewed; not executedPublished by Pipeworx

Vendor documentation

What you can do with it

Retrieve full prediction metadata and structure file URLs for a protein sequence
Get short summaries including organism and mean pLDDT scores
Fetch sequence-level annotations such as MUTAGEN or LOW_CONFIDENCE_REGIONS
Look up AlphaFold structure prediction metadata by UniProt accession

Source and maintenance

Community listingRegistry 0.2.1

mcp-registry: io.github.pipeworx-io/alphafold@0.2.1 Source repository Project website

Maintenance checked: Oct 31, 2026, 10:59 PM UTC

Packages and installation

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

@pipeworx/mcp-alphafold 0.2.1

npm

@pipeworx/mcp-alphafold package definition

{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-alphafold",
  "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.

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Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.

Cursor configuration

{
  "mcpServers": {
    "alphafold-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-alphafold@0.2.1"
      ],
      "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": {
    "alphafold-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-alphafold@0.2.1"
      ],
      "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": {
    "alphafold-mcp": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-alphafold@0.2.1"
      ],
      "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": {
    "alphafold-mcp": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-alphafold@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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