mcp-alphafold
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@mcp-alphafoldretrieve AlphaFold prediction for UniProt P04637"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
mcp-alphafold
AlphaFold predicted protein 3D structures (EBI)
Part of Pipeworx — an MCP gateway connecting AI agents to 250+ live data sources.
Tools
Tool | Description |
| Full prediction metadata + structure file URLs (PDB, CIF, PAE). |
| Short summary for a prediction (organism, sequence, mean pLDDT). |
| Sequence-level annotations (e.g. MUTAGEN, LOW_CONFIDENCE_REGIONS). |
| Alias for prediction — fetch by UniProt accession explicitly. |
Quick Start
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
{
"mcpServers": {
"alphafold": {
"url": "https://gateway.pipeworx.io/alphafold/mcp"
}
}
}Or connect to the full Pipeworx gateway for access to all 250+ data sources:
{
"mcpServers": {
"pipeworx": {
"url": "https://gateway.pipeworx.io/mcp"
}
}
}Using with ask_pipeworx
Instead of calling tools directly, you can ask questions in plain English:
ask_pipeworx({ question: "your question about Alphafold data" })The gateway picks the right tool and fills the arguments automatically.
More
License
MIT
This server cannot be installed
Resources
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