Query Alphafold

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

import 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
# take the URL from the API: AlphaFold DB serves only the latest version per entry,
# so a filename built from a pinned version number 404s after every release
def download_structure(uniprot_id, output_dir="/workspace/group", fmt="pdb"):
    entry = get_alphafold_prediction(uniprot_id)[0]
    url = entry[{"pdb": "pdbUrl", "cif": "cifUrl", "bcif": "bcifUrl"}[fmt]]
    r = requests.get(url)
    r.raise_for_status()
    filepath = f"{output_dir}/{url.rsplit('/', 1)[-1]}"
    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:
        entry = data[0]
        return {"cif_url": entry.get("cifUrl", ""), "pae_url": entry.get("paeDocUrl", ""), "data": entry}
    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 (mean pLDDT): {entry.get('globalMetricValue', 'N/A')}")
    print(f"PDB URL: {entry.get('pdbUrl', 'N/A')}")
    print(f"CIF URL: {entry.get('cifUrl', 'N/A')}")

Endpoints

Download Formats

Read pdbUrl, cifUrl, or bcifUrl off the prediction response rather than building a filename. AlphaFold DB serves only the latest version per entry -- AF-{UNIPROT_ID}-F1-model_v6.* today, with v4 and v5 both 404 -- so any pinned version breaks at the next release.

• PAE image: paeImageUrl; PAE matrix JSON: paeDocUrl

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?"