MCP server

Alphafold

io.github.pipeworx-io/alphafold

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

AlphaFold DB MCP — predicted protein structures.

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

46

Token cost

About 26,687 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http alphafold https://gateway.pipeworx.io/alphafold/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.alphafold]
url = "https://gateway.pipeworx.io/alphafold/mcp"

Gemini CLI

{"mcpServers":{"alphafold":{"httpUrl":"https://gateway.pipeworx.io/alphafold/mcp"}}}

Cursor

{"mcpServers":{"alphafold":{"url":"https://gateway.pipeworx.io/alphafold/mcp"}}}

VS Code

{"servers":{"alphafold":{"type":"http","url":"https://gateway.pipeworx.io/alphafold/mcp"}}}

Antigravity

agy mcp add alphafold https://gateway.pipeworx.io/alphafold/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"alphafold","server_url":"https://gateway.pipeworx.io/alphafold/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"alphafold","server_url":"https://gateway.pipeworx.io/alphafold/mcp"}

Tools

• annotations ~108 tokens
  Sequence-level annotations (e.g. MUTAGEN, LOW_CONFIDENCE_REGIONS).
• prediction ~90 tokens
  Full prediction metadata + structure file URLs (PDB, CIF, PAE).
• summary ~75 tokens
  Short summary for a prediction (organism, sequence, mean pLDDT).
• uniprot ~111 tokens
  Fetch AlphaFold structure prediction metadata (PDB/CIF/PAE download URLs, pLDDT scores) by UniProt accession (e.g. "P00533"); equivalent to `prediction` but takes uniprot_id explicitly.

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