Biohub ESM

Find ESM Atlas protein clusters whose representatives are most similar to a sequence, compared by ESMC sparse-autoencoder (SAE) feature profiles rather than by sequence alignment. Use it to find functional or structural neighbors of a protein. Takes a raw one-letter sequence up to 2,048 residues. Returns up to top_k representatives above a minimum similarity, so fewer may come back, each with a similarity score, cluster size, name, and a sequence to pass to the other ESM Atlas tools, plus the features most shared across hits. restricted_count is the number of hits withheld by safety screening. Hits without a stored structure may be predicted during the search, which can add time.

esm_atlas_search_similar_protein_clusters

Explain one ESMC sparse-autoencoder (SAE) feature by its index: its label, summary and description, category, activation pattern, example protein families, how often it occurs in UniRef90, the reviewed UniProt (Swiss-Prot) proteins that activate it most, and the most similar features. Use it when another ESM Atlas tool returns a feature_index worth understanding. It takes an index, not a sequence.

esm_atlas_get_sae_feature_detail

Get the ESM Atlas cluster a protein belongs to: cluster size, the share of members with characterized Pfam annotations, top Pfam domains, taxonomy and top phyla, and the SAE features typical of the cluster. ESM Atlas clusters group proteins by ESMC sparse-autoencoder (SAE) feature similarity, not by sequence identity. Use it to put a protein in context or judge how well studied its neighborhood is. Takes the raw one-letter sequence of a protein already in the ESM Atlas, such as a hit from esm_atlas_search_similar_protein_clusters; other sequences return not_found, because this tool computes nothing.

esm_atlas_get_cluster_info

Look up what the ESM Atlas knows about one protein sequence: its source accession, the confidence of its predicted structure (pTM and mean pLDDT), whether a structure exists or can be predicted (up to 700 residues), and its strongest ESMC sparse-autoencoder (SAE) features, which are learned, labeled protein properties, with the residue ranges that drive them. Use it first for a sequence you already have. Takes a raw one-letter sequence; resolve a protein name or accession with esm_atlas_search_uniprot or esm_atlas_lookup_accession. Sequences not in the ESM Atlas get features computed for up to 2,048 residues. This tool never predicts a structure; ui_show_protein_structure with the same sequence shows one. No saved ID or download is created.

esm_atlas_get_protein_details

Get the amino-acid sequence for a UniParc (UPI...), MGnify (MGYP...), or IMG gene ID, to pass to the ESM Atlas tools. Use it when a protein is identified by one of those IDs. UniProt accessions and entry names are not accepted here; esm_atlas_search_uniprot looks them up. Other formats return invalid_input.

esm_atlas_lookup_accession

Find proteins in UniProt by name, gene, organism, function, or accession, and get their sequences for the ESM Atlas tools. Use it when a protein is named rather than given as a sequence. Accepts free text, such as "human hemoglobin alpha", or UniProt query syntax, such as "gene:TP53 AND organism_id:9606 AND reviewed:true"; a UniProt accession (P69905) or entry name (HBA_HUMAN) is looked up directly. Returns up to size entries with accession, name, gene, organism, function, and sequence, plus the total number of matches. For UniParc, MGnify, or IMG IDs, use esm_atlas_lookup_accession.

esm_atlas_search_uniprot

View a protein's 3D structure from its amino-acid sequence. Use it when the user wants to see or visualize a structure, or when you need to look at one to answer a question about its shape. Pass the raw one-letter sequence; for a protein name or accession, get the sequence first with esm_atlas_search_uniprot or esm_atlas_lookup_accession. Returns the ESM Atlas structure when one exists, or predicts one for sequences up to 700 residues; longer sequences not in the ESM Atlas return sequence_too_long_to_fold. Structures are computational predictions, not experimental. The result includes a PNG preview you can see and, in clients that support MCP Apps, an interactive viewer the user can rotate, recolor, and select residues in without another call. Nothing is saved and no link is created. Without a preview image, don't describe how the structure looks.

ui_show_protein_structure