AlphaFold Structure Database Query
Query the AlphaFold EBI API for predicted protein structures.
When to Use
- User asks about a protein's predicted 3D structure
- User wants to download PDB/CIF structure files
- User asks about structure confidence (pLDDT scores)
- User wants to visualize protein structure
How to Execute
pythonimport requests import json BASE_URL = "https://alphafold.ebi.ac.uk/api" # 1. Get prediction info def get_alphafold_prediction(uniprot_id): url = f"{BASE_URL}/prediction/{uniprot_id}" r = requests.get(url) r.raise_for_status() return r.json() # 2. Download structure file def download_structure(uniprot_id, output_dir="/workspace/group", fmt="pdb", version="v4"): filename = f"AF-{uniprot_id}-F1-model_{version}.{fmt}" url = f"https://alphafold.ebi.ac.uk/files/{filename}" r = requests.get(url) r.raise_for_status() filepath = f"{output_dir}/{filename}" with open(filepath, 'wb') as f: f.write(r.content) return filepath # 3. Get per-residue confidence (pLDDT) def get_plddt(uniprot_id): url = f"{BASE_URL}/prediction/{uniprot_id}" r = requests.get(url) data = r.json() if isinstance(data, list) and data: cif_url = data[0].get("cifUrl", "") plddt_url = data[0].get("paeImageUrl", "") return {"cifUrl": cif_url, "paeImageUrl": plddt_url, "data": data[0]} return data # Example data = get_alphafold_prediction("P04637") # TP53 if isinstance(data, list) and data: entry = data[0] print(f"UniProt: {entry.get('uniprotAccession')}") print(f"Gene: {entry.get('gene', 'N/A')}") print(f"Organism: {entry.get('organismScientificName', 'N/A')}") print(f"Model confidence: {entry.get('globalMetricValue', 'N/A')}") print(f"PDB URL: {entry.get('pdbUrl', 'N/A')}") print(f"CIF URL: {entry.get('cifUrl', 'N/A')}")
Endpoints
| Endpoint | URL | Use |
|---|---|---|
| Prediction | /api/prediction/{uniprot_id} | Get model info & download URLs |
| Summary | /api/uniprot/summary/{uniprot_id}.json | Brief summary |
| Annotations | /api/annotations/{uniprot_id} | Per-residue annotations |
Download Formats
- PDB:
AF-{UNIPROT_ID}-F1-model_v4.pdb - CIF:
AF-{UNIPROT_ID}-F1-model_v4.cif - PAE image: Available from prediction endpoint
Follow-up Suggestions
- "Want me to analyze the structure confidence by region?"
- "Should I compare this to the experimental PDB structure?"
- "Want me to identify disordered regions?"
