Biohub ESM

biohub-esm

Route Biohub ESM requests to ESMC, ESMFold2, ESM Atlas, Modal, or private open weights. Use for explicitly ESM/Biohub work, ESM protein representations or mutation scoring, ESMFold2 folding, Atlas discovery, showing a protein's 3D structure in the Biohub MCP's Mol* viewer, or choosing an ESM compute route. Do not use for unrelated non-ESM models, generic sequence alignment, or opening a local structure file in a non-Biohub viewer unless the user explicitly asks to compare it with Biohub ESM.

biohub-esm-setup

Set up and preflight Biohub ESM, Atlas, Modal, and Hugging Face access. Use when installing pinned ESM dependencies, checking credentials, connecting the Biohub MCP for Atlas tools and its Mol* structure viewer, or fixing auth, rate-limit, credits, PATH, SDK, or GPU setup. Never ask for secret values.

esm-atlas

Use 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. Also use for the full Atlas feature catalog, thumbnails, batch jobs, MD5-only records, or anonymous S3 data, which stay on the plugin script. Use ESMC instead to extract SAE activations with a chosen ESMC checkpoint. Atlas is public data, not a model to deploy, and needs no client key.

esmc

Use 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. Sequence only; not for folding, Atlas lookup, or calling an untrained classifier predictive.

esmfold2

Use 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. Not for dynamics, experimental truth, or Atlas discovery.