Documentation Index
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Resolve a UniProt accession, retrieve its Atlas protein record, and inspect its feature-based cluster.
Resolve the UniProt accession
import httpx
base_url = "https://biohub.ai/esm/protein/api/v1alpha1"
with httpx.Client(timeout=60) as client:
response = client.get(f"{base_url}/uniprot/P24941")
response.raise_for_status()
resolved = response.json()
protein_hash = resolved["protein_hash"]
print(resolved["accession"], resolved["protein_name"], protein_hash)
Retrieve the protein record
with httpx.Client(timeout=60) as client:
response = client.get(
f"{base_url}/proteins/{protein_hash}",
params={"topk_features": 5, "fold_on_miss": False},
)
response.raise_for_status()
protein = response.json()
print(protein["accession"], protein["sequence_length"])
for feature in protein["sae_features"]:
print(feature["feature_index"], feature["label"])
ptm and mean_plddt are None when the Atlas has no stored structure for this exact sequence.
Read the protein endpoint reference before changing feature selection or on-demand folding options.Find the nearest cluster representative
cluster_hash = protein["cluster_rep_protein_hash"]
if cluster_hash is None:
with httpx.Client(timeout=120) as client:
response = client.get(
f"{base_url}/similarity-search",
params={
"sequence": resolved["sequence"],
"topk_results": 1,
"include_cluster_info": True,
},
)
response.raise_for_status()
nearest = response.json()["similar_proteins"][0]
cluster_hash = nearest["protein_hash"]
print(nearest["protein_name"], "similarity", round(nearest["similarity_score"], 3))
cluster_rep_protein_hash.
Most UniProt proteins don’t, so the code uses the nearest cluster representative by SAE feature similarity instead.Retrieve the cluster report
with httpx.Client(timeout=60) as client:
response = client.get(f"{base_url}/clusters/{cluster_hash}")
response.raise_for_status()
cluster = response.json()
print("Cluster size:", cluster["cluster_size"])
print("Characterized percent:", cluster["cluster_pct_characterized"])
print("Top Pfam domains:", cluster["cluster_top_pfam_domains"])
print("Taxonomy:", cluster["cluster_taxonomy_info"])