# Alphafold [Health: Active]

**Category:** 🧬 Biology & Bioinformatics  
**Repository:** https://github.com/pipeworx-io/mcp-alphafold  
**GitHub Stars:** 1  
**npm Downloads (last month):** 462  
**Views:** 1  
**Installs:** 0  
**Upvotes:** 0  
**Directory Page:** https://allmcps.com/mcp/alphafold

## Description
AlphaFold DB MCP — predicted protein structures.

## Tools
Capabilities this server exposes over MCP:

- **prediction**

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `npx` (confidence: high):

```json
"mcpServers": {
  "alphafold": {
    "command": "npx",
    "args": ["-y","@pipeworx/mcp-alphafold"]
  }
}
```

## Documentation

## What the Alphafold MCP server does

The Alphafold MCP server connects MCP clients to the EBI AlphaFold Protein Structure Database, which provides predicted three-dimensional protein structures for approximately 214 million sequences. Queries use a UniProt accession, such as `P00533`, as the primary identifier.

The integration is an independent, unofficial connection to the upstream database. It is intended for retrieving existing AlphaFold predictions and related records, not for running new structure predictions.

## How it works

The server reads data from the AlphaFold Database API at `https://alphafold.ebi.ac.uk/api/`. Its MCP tools accept structured arguments and return database results to the connected agent. A prediction lookup includes complete prediction metadata and URLs for available PDB, CIF, and PAE files.

The gateway version is available at `https://gateway.pipeworx.io/alphafold/mcp`. That endpoint lists the Alphafold tools together with shared Pipeworx tools, including routing and discovery capabilities. The full Pipeworx gateway is another connection option when an agent needs direct access to the broader catalog of data sources.

A local process uses MCP over standard input and output. In that mode, the server exposes only the Alphafold pack's tools and does not add the gateway's shared meta-tools or cross-catalog routing.

## Setup and configuration

To run the Alphafold MCP server locally, configure an MCP client to launch `npx -y @pipeworx/mcp-alphafold`. This option does not require a Pipeworx account or a gateway round trip. Running the same command directly can verify that the process starts.

For a hosted connection, add the gateway URL as an MCP server endpoint. The README provides configurations for Claude Desktop, Cursor, and Windsurf. The gateway is keyless, and the documented HTTP interface states that no account is needed for the first calls.

The tools can also be called over HTTP. For example, send a JSON POST request to `/v1/tools/alphafold_prediction` with a `qualifier` containing a UniProt accession. The gateway also provides endpoints for inspecting tools and searching available packs.

## Tools and capabilities

The Alphafold MCP server exposes these database-oriented operations:

- `prediction(qualifier)` returns full prediction metadata and file URLs.
- `summary(qualifier)` returns a shorter structure summary.
- `annotations(qualifier, type?)` returns sequence-level annotations, including regions with low pLDDT when available.
- `uniprot(uniprot_id)` performs the prediction lookup using an explicit UniProt accession.

On a gateway connection, `tools/list` also includes shared Pipeworx tools. `ask_pipeworx` can accept a plain-language question and route it to an appropriate tool, while discovery and search tools help locate other catalog capabilities. These shared tools are not present in the standalone stdio process.

## Limitations and notes

The Alphafold MCP server depends on records available from the EBI AlphaFold Protein Structure Database and does not generate predictions itself. The `qualifier` argument should be a UniProt accession; use the explicit `uniprot` operation when that form is preferable.

The number of tools shown by the hosted endpoint is larger than the four Alphafold-specific operations because shared gateway tools are included. The connection's `initialize` response is the authoritative description of its current scope. The gateway and local modes use the same underlying source and pack tools, but only the gateway provides Pipeworx-wide routing through its shared meta-tools.

_Full upstream README: https://allmcps.com/mcp/alphafold/readme_