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Biohub MCP connects your AI assistant to the ESM Atlas through the Model Context Protocol. Your assistant can look up a protein, find proteins with similar ESMC sparse autoencoder (SAE) features, explain what those features mean, and show the structure in an interactive Mol* viewer. There is nothing to install, and you don’t need a Biohub account or an API key.

Quickstart

Add the server to your client and run a first request in a few minutes.

Connect your client

Setup steps for ChatGPT, Codex, Claude, Cursor, VS Code, and other clients.

Example prompts

Prompts to copy, with the tools they use and what to expect back.

ESM Atlas tools

Inputs, outputs, limits, and errors for every tool.

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What you can do

  • Turn a protein name or a UniProt, UniParc, MGnify, or IMG accession into an amino-acid sequence.
  • Find ESM Atlas cluster representatives whose SAE feature profiles are closest to your protein, optionally only clusters with no characterized Pfam domains.
  • See a protein’s strongest SAE features, the residues that drive them, and what each feature means.
  • Summarize a cluster: its size, how well characterized it is, its Pfam domains, and its most common phyla.
  • View a stored or newly predicted structure, colored by chain or by confidence, with the residues you care about highlighted.

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Connection details

Opening the URL in a browser shows 405 Method Not Allowed. That is expected, because MCP clients send POST requests to it.

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Tools at a glance

Biohub MCP has seven tools. All of them are marked read-only: they look things up and compute results, but they create no saved items, IDs, or links for you. The structure viewer is an MCP App that supported hosts draw inline. Your client may show the tools with a prefix, such as mcp__biohub__esm_atlas_search_uniprot. See the ESM Atlas tools and Structure viewer references for the details.

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How it works

You ask a question in your AI client. The assistant decides which tools to call and passes results from one tool to the next. For example, a UniProt search returns a sequence, and the similarity search, protein details, and structure viewer all accept that sequence directly. When the ESM Atlas has no stored result for a sequence, some tools compute SAE features or predict a structure on the spot, which takes longer. Security and privacy explains when that happens and which services receive your queries.

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MCP or REST API?

The MCP tools and the REST endpoints cover similar ground, but their inputs and outputs differ. For example, the MCP tools take raw sequences, while several REST endpoints take a protein hash.

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Next steps