AlphaFold Database

Programmatic access to DeepMind's AlphaFold Protein Structure Database (200M+ predicted structures).

Quick Reference

# Fetch structure via Biopython
from Bio.PDB import alphafold_db
predictions = list(alphafold_db.get_predictions("P00520"))
alphafold_db.download_cif_for(predictions[0], directory="./output")

# Direct API call
import requests
resp = requests.get("https://alphafold.ebi.ac.uk/api/prediction/P00520")
entry_id = resp.json()[0]['entryId']  # AF-P00520-F1

# Download structure file
structure_url = f"https://alphafold.ebi.ac.uk/files/{entry_id}-model_v4.cif"

When to Use

• Obtain 3D coordinates for proteins without experimental structures
• Assess prediction quality via pLDDT and PAE metrics
• Download structure files (mmCIF, PDB) for visualization or docking
• Retrieve proteome-scale datasets for computational analysis

Key Concepts

Term	Description
UniProt Accession	Protein identifier (e.g., P00520) used to query
AlphaFold ID	Format: AF-{UniProt}-F{fragment} (e.g., AF-P00520-F1)
pLDDT	Per-residue confidence (0-100); >90 = reliable, <50 = disordered
PAE	Predicted Aligned Error; <5A = high confidence domain positions

See references/confidence-scores.md for detailed interpretation guidance.

File Types

File	URL Pattern	Contents
Coordinates	{id}-model_v4.cif	Atomic positions (mmCIF)
Confidence	{id}-confidence_v4.json	Per-residue pLDDT array
PAE Matrix	{id}-predicted_aligned_error_v4.json	Inter-residue error

Base URL: https://alphafold.ebi.ac.uk/files/

Core Operations

Fetch Structure Metadata

import requests
resp = requests.get(f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}")
metadata = resp.json()[0]
af_id = metadata['entryId']

Download All Files

Use scripts/alphafold_utils.py:

from scripts.alphafold_utils import download_alphafold_files
paths = download_alphafold_files("AF-P04637-F1", output_dir="./data")

Analyze Confidence

from scripts.alphafold_utils import get_plddt_scores
stats = get_plddt_scores("AF-P04637-F1")
print(f"Average pLDDT: {stats['mean']:.1f}")

Bulk Proteome Access

# Google Cloud Storage
gsutil ls gs://public-datasets-deepmind-alphafold-v4/
gsutil -m cp "gs://public-datasets-deepmind-alphafold-v4/proteomes/proteome-tax_id-9606-*.tar" ./

See references/bulk-access.md for BigQuery queries and batch processing.

Caveats

• Predictions, not experiments: Verify critical findings experimentally
• Confidence matters: Always check pLDDT before using regions
• Single chains only: No multimers or complexes
• No ligands: Missing cofactors, ions, PTMs

Setup

pip install biopython requests numpy matplotlib pandas scipy
# Optional: pip install google-cloud-bigquery gsutil

Links

• Database: https://alphafold.ebi.ac.uk/
• API Docs: https://alphafold.ebi.ac.uk/api-docs
• Biopython: https://biopython.org/docs/dev/api/Bio.PDB.alphafold_db.html