Biohub ESM

What you can ask

• Map the mutational landscape of PETase and show me where it is most constrained or tolerant.Copy

  Example path ui_show_protein_structure · Biohub ESM Router skill

• Show me what ESMC has learned about ATP synthase and map the strongest features onto its structure.
• Model how a modified GLP-1 peptide with a lipid linker might engage GLP-1R, then show me the complex.

MCP connector

Server URL

https://biohub.ai/mcpCopy

Login

None

Protocol

MCP 2026-07-28 · Interactive UI

Instructions

Biohub MCP provides ESM Atlas discovery and Mol* viewing. Search UniProt or resolve an accession for a sequence. Protein details may infer features; similarity search may infer features and fold missing neighbors; viewing may fold. Honor rate_limited retry guidance and never automatically retry indeterminate compute outcomes. Results are response-local, and separate requests may compute again. Model predictions are hypotheses, not experimental validation. When a request matches a Skill route below, read that exact MCP resource before searching for or calling Biohub tools, then follow the Skill and only the supporting resources it directs you to. If native MCP resource reads are unavailable, use the read_resource tool with the same URI. Use list_resources to discover enabled resources. Do not infer a workflow from tool names alone. Skill routes:

skill://waveorder-tutorial/SKILL.md: Interactively walk a user through their first waveorder reconstruction on their own computer, from raw imaging data to a tuned result.

skill://waveorder-visualize-otf/SKILL.md: Compute a waveorder transfer function (OTF) from a reconstruction config on the user's own computer and open it in napari.

Tools

Skills

5 in the ChatGPT listing

• Biohub ESM RouterRoute Biohub ESM requests to ESMC, ESMFold2, ESM Atlas, Modal, or private open weights.
• Biohub ESM SetupSet up and preflight Biohub ESM, Atlas, Modal, and Hugging Face access.
• ESM AtlasUse when the user wants proteins similar to a protein, a protein name or accession resolved to a sequence, an Atlas record, SAE feature profile, or cluster context for a sequence, one Atlas SAE feature explained, or a protein structure viewed, all through the public Biohub MCP.
• ESMCUse when the user needs ESMC embeddings, hidden states, logits, entropy, zero-shot mutation scoring, SAE features, fitted heads, or fine-tuning, or wants to see an analyzed protein's highlighted residues again in the Biohub MCP structure view.
• ESMFold2Use when the user needs ESMFold2 all-atom folding for proteins, DNA, RNA, modified residues, or ligands, including Fast/full routing, MSA, confidence, structures, and provenance.