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Alphafold

Queries AlphaFold DB for predicted protein structures, metadata, annotations, and structure file URLs over MCP.

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Install Alphafold

Pick your client, then add it in one click or paste the config.

STDIONode.js
~/Library/Application Support/Claude/claude_desktop_config.json
claude_desktop_config.json
{
  "mcpServers": {
    "alphafold": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-alphafold"
      ]
    }
  }
}

Settings → Developer → Edit Config, merge this into mcpServers, then fully quit and reopen Claude Desktop.

We couldn’t confirm it starts correctly

The install command started, but didn't respond the way we expected when we tried to talk to it.

npx -y @pipeworx/mcp-alphafold

initialize succeeded but no response to tools/list.

This is an experimental automated check and can have false negatives — missing environment variables, a slow cold install, etc. It doesn’t necessarily mean something’s wrong. Last checked Today.

Overview

The Alphafold MCP server retrieves predicted protein structure data from the EBI AlphaFold Protein Structure Database. It accepts UniProt accessions and exposes tools for prediction metadata, summaries, sequence annotations, and UniProt-specific lookups. Use it when an agent needs structure records or links to PDB, CIF, or PAE files without an API key. It can run locally over stdio or through the Pipeworx gateway.

Use cases

  • Retrieve predicted protein structure metadata by UniProt accession
  • Find PDB, CIF, and PAE file URLs
  • Inspect low-confidence sequence regions
  • Ask an agent for a concise structure summary
  • Query AlphaFold records through a local stdio process

Key features

  • Prediction metadata and structure file URLs
  • Short protein structure summaries
  • Sequence-level annotation lookups
  • Explicit UniProt accession queries
  • Local stdio and hosted gateway modes
  • HTTP tool invocation

Tools1

What Alphafold lets your agent do. Expand a tool for its parameters.

Self-reported~3 tokens of context

Security & health

What it can reach and how reliably it runs — from our own checks, not the maintainer’s claims.

ActiveLast checked 2d ago

Recent health check succeeded.

8/8 checks healthy over the last 45d

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 15d ago via OSV.dev · @pipeworx/mcp-alphafold (npm)

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

GitHub stars1Stargazers on the source repository.
npm downloads462Package downloads in the last 30 days.
Last commit4d agoMost recent push to the default branch.
Install checkInconclusiveStarted but did not complete the MCP handshake in our test.
Tools exposed1Callable tools this server registers over MCP.
Directory activity1 viewsConfig copies, upvotes, and views on AllMCPs.

How Alphafold works

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.

Read the full README View source on GitHub

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Frequently Asked Questions about Alphafold

Alphafold is an MCP server that connects AI agents to the EBI AlphaFold Protein Structure Database. Its main tools retrieve prediction metadata and structure file URLs, provide short summaries, return sequence annotations, and look up records by explicit UniProt accession. It accesses existing predicted structures rather than generating new predictions.

Install it by configuring your MCP client to run `npx -y @pipeworx/mcp-alphafold`. This starts the standalone stdio server locally and requires no Pipeworx account. You can also connect an MCP client to `https://gateway.pipeworx.io/alphafold/mcp` instead of running the package locally.

Yes, Alphafold works with Cursor. Add the hosted MCP URL `https://gateway.pipeworx.io/alphafold/mcp` to Cursor's MCP configuration, or configure Cursor to launch the local `npx -y @pipeworx/mcp-alphafold` process.

The server accepts a UniProt accession as the `qualifier`, such as `P00533`. The `uniprot` tool takes the accession in its `uniprot_id` argument, while the other database tools use the qualifier form.

No, the integration is keyless. The hosted gateway documentation also says that no account is needed for the first calls, while the standalone package runs locally without a Pipeworx account.

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