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The Biohub MCP connects your AI assistant to the ESM Atlas and to the ESMFold2 and ESMC models on the Biohub Platform through the Model Context Protocol server. You ask your AI assistant a question, and the assistant decides which MCP tools (a callable function) to call and passes results from one tool to the next. Its ESM Atlas tools give your assistant the same abilities as the ESM Atlas Agent, the “Ask the atlas” box on the ESM Atlas site.

What the MCP server can do

  • Turn a protein name or a UniProt, UniParc, or MGnify 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.
  • View a stored or newly predicted structure, colored by chain or by confidence, with the residues you care about highlighted.
  • Fold and view a complex of proteins, DNA, RNA, and small molecules; see Complexes.
  • Fold proteins and complexes of up to 4,096 tokens with ESMFold2 and get confidence scores, including at maximum accuracy; see Folding tools.

Get started

Quickstart

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

Example prompts

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

Skills

Step-by-step instructions your client follows, such as reconstructing microscopy data with WaveOrder.

ESM Atlas tools

Look up a protein, its SAE features, and similar proteins in the ESM Atlas, and read the results.

Structure viewer

Show a structure in an interactive Mol* viewer, then export it.
Connect to the MCP by signing in your browser with a free Biohub account. Atlas tools are free, and folds and ESMC scoring are billed to that account. A tool is a named action the Biohub MCP can carry out. Folding and ESMC tools start billed work on the Biohub Platform; only queued folds create a run you can read later. Your client may add a prefix to tool names, such as mcp__biohub__esm_atlas_search_uniprot. The viewer can fold a billed complex, so it is marked compute and non-idempotent, like the folding and ESMC tools. See Why some calls take longer for what clients may ask you to approve.

ESM Atlas tools

Atlas tools are free to use, and can look up information and compute results without creating saved items or IDs. See ESM Atlas tools for inputs, results, and errors.

Structure viewer

See Structure viewer for view options and export.

Folding tools

See Folding tools for how a fold runs and how to read the scores.

Mutation scoring tools

See Mutation scoring tools for inputs, results, and costs.

Resource tools

See MCP resource reference for inputs, limits, and errors.

MCP server vs. REST APIs

You can complete similar tasks using the Biohub MCP server or the ESM Atlas and Biohub Platform APIs, but the inputs and outputs differ. For example, the MCP tools take raw sequences, while several REST endpoints take a protein hash, and the folding tools return scores but not the structure files the API returns. Choose the Biohub MCP when you are working with an AI client and you want the assistant to choose the best tool. Use the APIs when you are writing code or creating workflows that need fixed requests, direct access to responses, or greater control over your results. The Biohub Platform APIs need an API key; the MCP tools use your sign-in instead.

Next steps