alterlab-alphafold-db

AlphaFold Database

Overview

AlphaFold DB is a public repository of AI-predicted 3D protein structures for over 200 million proteins, maintained by DeepMind and EMBL-EBI. Access structure predictions with confidence metrics, download coordinate files, retrieve bulk datasets, and integrate predictions into computational workflows.

When to Use This Skill

This skill should be used when working with AI-predicted protein structures in scenarios such as:

• Retrieving protein structure predictions by UniProt ID or protein name
• Downloading PDB/mmCIF coordinate files for structural analysis
• Analyzing prediction confidence metrics (pLDDT, PAE) to assess reliability
• Accessing bulk proteome datasets via Google Cloud Platform
• Comparing predicted structures with experimental data
• Performing structure-based drug discovery or protein engineering
• Building structural models for proteins lacking experimental structures
• Integrating AlphaFold predictions into computational pipelines

Core Capabilities

1. Searching and Retrieving Predictions

Using Biopython (Recommended):

The Biopython library provides the simplest interface for retrieving AlphaFold structures:

from Bio.PDB import alphafold_db

# Get all predictions for a UniProt accession
predictions = list(alphafold_db.get_predictions("P00520"))

# Download structure file (mmCIF format)
for prediction in predictions:
    cif_file = alphafold_db.download_cif_for(prediction, directory="./structures")
    print(f"Downloaded: {cif_file}")

# Get Structure objects directly
from Bio.PDB import MMCIFParser
structures = list(alphafold_db.get_structural_models_for("P00520"))

Direct API Access:

Query predictions using REST endpoints:

import requests

# Get prediction metadata for a UniProt accession
uniprot_id = "P00520"
api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"
response = requests.get(api_url)
prediction_data = response.json()

# Extract AlphaFold ID
alphafold_id = prediction_data[0]['entryId']
print(f"AlphaFold ID: {alphafold_id}")

Using UniProt to Find Accessions:

Search UniProt to find protein accessions first:

import requests, time

def get_uniprot_ids(query, from_db='PDB', to_db='UniProtKB'):
    """Map IDs to UniProt accessions via the current REST API.

    from_db/to_db must be current DB names, e.g. 'PDB', 'Gene_Name',
    'UniProtKB_AC-ID', 'UniProtKB'.
    Valid values: https://rest.uniprot.org/configure/idmapping/fields
    """
    base = 'https://rest.uniprot.org'
    # 1) submit job
    r = requests.post(f'{base}/idmapping/run',
                      data={'from': from_db, 'to': to_db, 'ids': query})
    r.raise_for_status()
    job_id = r.json()['jobId']
    # 2) poll status
    while True:
        s = requests.get(f'{base}/idmapping/status/{job_id}').json()
        if s.get('jobStatus') in (None, 'FINISHED') or 'results' in s:
            break
        if s.get('jobStatus') in ('ERROR',):
            raise RuntimeError(s)
        time.sleep(1)
    # 3) fetch results
    res = requests.get(f'{base}/idmapping/results/{job_id}').json()
    return [m['to'] for m in res.get('results', [])]

# Example: Find UniProt accessions for a gene name
protein_ids = get_uniprot_ids("HBB", from_db="Gene_Name", to_db="UniProtKB")

2. Downloading Structure Files

AlphaFold provides multiple file formats for each prediction:

File Types Available:

• Model coordinates (model_v4.cif): Atomic coordinates in mmCIF/PDBx format
• Confidence scores (confidence_v4.json): Per-residue pLDDT scores (0-100)
• Predicted Aligned Error (predicted_aligned_error_v4.json): PAE matrix for residue pair confidence

Download URLs:

import requests

alphafold_id = "AF-P00520-F1"
version = "v4"

# Model coordinates (mmCIF)
model_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.cif"
response = requests.get(model_url)
with open(f"{alphafold_id}.cif", "w") as f:
    f.write(response.text)

# Confidence scores (JSON)
confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_{version}.json"
response = requests.get(confidence_url)
confidence_data = response.json()

# Predicted Aligned Error (JSON)
pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_{version}.json"
response = requests.get(pae_url)
pae_data = response.json()

PDB Format (Alternative):

# Download as PDB format instead of mmCIF
pdb_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.pdb"
response = requests.get(pdb_url)
with open(f"{alphafold_id}.pdb", "wb") as f:
    f.write(response.content)

3. Working with Confidence Metrics

AlphaFold predictions include confidence estimates critical for interpretation:

pLDDT (per-residue confidence):

import json
import requests

# Load confidence scores
alphafold_id = "AF-P00520-F1"
confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
confidence = requests.get(confidence_url).json()

# Extract pLDDT scores
plddt_scores = confidence['confidenceScore']

# Interpret confidence levels
# pLDDT > 90: Very high confidence
# pLDDT 70-90: High confidence
# pLDDT 50-70: Low confidence
# pLDDT < 50: Very low confidence

high_confidence_residues = [i for i, score in enumerate(plddt_scores) if score > 90]
print(f"High confidence residues: {len(high_confidence_residues)}/{len(plddt_scores)}")

PAE (Predicted Aligned Error):

PAE indicates confidence in relative domain positions:

import numpy as np
import matplotlib.pyplot as plt

# Load PAE matrix
pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_v4.json"
pae = requests.get(pae_url).json()

# Visualize PAE matrix
# The AlphaFold PAE endpoint returns a single-element JSON array, so index [0]
# before the key. (If a future response returns a bare object, drop the [0].)
pae_matrix = np.array(pae[0]['predicted_aligned_error'])
plt.figure(figsize=(10, 8))
plt.imshow(pae_matrix, cmap='viridis_r', vmin=0, vmax=30)
plt.colorbar(label='PAE (Å)')
plt.title(f'Predicted Aligned Error: {alphafold_id}')
plt.xlabel('Residue')
plt.ylabel('Residue')
plt.savefig(f'{alphafold_id}_pae.png', dpi=300, bbox_inches='tight')

# Low PAE values (<5 Å) indicate confident relative positioning
# High PAE values (>15 Å) suggest uncertain domain arrangements

4. Bulk Data Access via Google Cloud

For large-scale analyses, use Google Cloud datasets:

Google Cloud Storage:

# Install gsutil
uv pip install gsutil

# List available data
gsutil ls gs://public-datasets-deepmind-alphafold-v4/

# Download entire proteomes (by taxonomy ID)
gsutil -m cp gs://public-datasets-deepmind-alphafold-v4/proteomes/proteome-tax_id-9606-*.tar .

# Download specific files
gsutil cp gs://public-datasets-deepmind-alphafold-v4/accession_ids.csv .

BigQuery Metadata Access:

from google.cloud import bigquery

# Initialize client
client = bigquery.Client()

# Query metadata
query = """
SELECT
  entryId,
  uniprotAccession,
  organismScientificName,
  globalMetricValue,
  fractionPlddtVeryHigh
FROM `bigquery-public-data.deepmind_alphafold.metadata`
WHERE organismScientificName = 'Homo sapiens'
  AND fractionPlddtVeryHigh > 0.8
LIMIT 100
"""

results = client.query(query).to_dataframe()
print(f"Found {len(results)} high-confidence human proteins")

Download by Species:

⚠️ Security Note: The example below uses shell=True for simplicity. In production environments, prefer using subprocess.run() with a list of arguments to prevent command injection vulnerabilities. See Python subprocess security.

import subprocess
import shlex

def download_proteome(taxonomy_id, output_dir="./proteomes"):
    """Download all AlphaFold predictions for a species"""
    # Validate taxonomy_id is an integer to prevent injection
    if not isinstance(taxonomy_id, int):
        raise ValueError("taxonomy_id must be an integer")
    
    pattern = f"gs://public-datasets-deepmind-alphafold-v4/proteomes/proteome-tax_id-{taxonomy_id}-*_v4.tar"
    # Use list form instead of shell=True for security
    subprocess.run(["gsutil", "-m", "cp", pattern, f"{output_dir}/"], check=True)

# Download E. coli proteome (tax ID: 83333)
download_proteome(83333)

# Download human proteome (tax ID: 9606)
download_proteome(9606)

5. Parsing and Analyzing Structures

Work with downloaded AlphaFold structures using BioPython:

from Bio.PDB import MMCIFParser, PDBIO
import numpy as np

# Parse mmCIF file
parser = MMCIFParser(QUIET=True)
structure = parser.get_structure("protein", "AF-P00520-F1-model_v4.cif")

# Extract coordinates
coords = []
for model in structure:
    for chain in model:
        for residue in chain:
            if 'CA' in residue:  # Alpha carbons only
                coords.append(residue['CA'].get_coord())

coords = np.array(coords)
print(f"Structure has {len(coords)} residues")

# Calculate distances
from scipy.spatial.distance import pdist, squareform
distance_matrix = squareform(pdist(coords))

# Identify contacts (< 8 Å)
contacts = np.where((distance_matrix > 0) & (distance_matrix < 8))
print(f"Number of contacts: {len(contacts[0]) // 2}")

Extract B-factors (pLDDT values):

AlphaFold stores pLDDT scores in the B-factor column:

from Bio.PDB import MMCIFParser

parser = MMCIFParser(QUIET=True)
structure = parser.get_structure("protein", "AF-P00520-F1-model_v4.cif")

# Extract pLDDT from B-factors
plddt_scores = []
for model in structure:
    for chain in model:
        for residue in chain:
            if 'CA' in residue:
                plddt_scores.append(residue['CA'].get_bfactor())

# Identify high-confidence regions
high_conf_regions = [(i, score) for i, score in enumerate(plddt_scores, 1) if score > 90]
print(f"High confidence residues: {len(high_conf_regions)}")

6. Batch Processing Multiple Proteins

Process multiple predictions efficiently:

from Bio.PDB import alphafold_db
import pandas as pd

uniprot_ids = ["P00520", "P12931", "P04637"]  # Multiple proteins
results = []

for uniprot_id in uniprot_ids:
    try:
        # Get prediction
        predictions = list(alphafold_db.get_predictions(uniprot_id))

        if predictions:
            pred = predictions[0]

            # Download structure
            cif_file = alphafold_db.download_cif_for(pred, directory="./batch_structures")

            # Get confidence data
            alphafold_id = pred['entryId']
            conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
            conf_data = requests.get(conf_url).json()

            # Calculate statistics
            plddt_scores = conf_data['confidenceScore']
            avg_plddt = np.mean(plddt_scores)
            high_conf_fraction = sum(1 for s in plddt_scores if s > 90) / len(plddt_scores)

            results.append({
                'uniprot_id': uniprot_id,
                'alphafold_id': alphafold_id,
                'avg_plddt': avg_plddt,
                'high_conf_fraction': high_conf_fraction,
                'length': len(plddt_scores)
            })
    except Exception as e:
        print(f"Error processing {uniprot_id}: {e}")

# Create summary DataFrame
df = pd.DataFrame(results)
print(df)

Installation and Setup

Python Libraries

# Install Biopython for structure access
uv pip install biopython

# Install requests for API access
uv pip install requests

# For visualization and analysis
uv pip install numpy matplotlib pandas scipy

# For Google Cloud access (optional)
uv pip install google-cloud-bigquery gsutil

3D-Beacons API Alternative

AlphaFold can also be accessed via the 3D-Beacons federated API:

import requests

# Query via 3D-Beacons
uniprot_id = "P00520"
url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json"
response = requests.get(url)
data = response.json()

# Filter for AlphaFold structures
af_structures = [s for s in data['structures'] if s['provider'] == 'AlphaFold DB']

Common Use Cases

Structural Proteomics

• Download complete proteome predictions for analysis
• Identify high-confidence structural regions across proteins
• Compare predicted structures with experimental data
• Build structural models for protein families

Drug Discovery

• Retrieve target protein structures for docking studies
• Analyze binding site conformations
• Identify druggable pockets in predicted structures
• Compare structures across homologs

Protein Engineering

• Identify stable/unstable regions using pLDDT
• Design mutations in high-confidence regions
• Analyze domain architectures using PAE
• Model protein variants and mutations

Evolutionary Studies

• Compare ortholog structures across species
• Analyze conservation of structural features
• Study domain evolution patterns
• Identify functionally important regions

Key Concepts

UniProt Accession: Primary identifier for proteins (e.g., "P00520"). Required for querying AlphaFold DB.

AlphaFold ID: Internal identifier format: AF-[UniProt accession]-F[fragment number] (e.g., "AF-P00520-F1").

pLDDT (predicted Local Distance Difference Test): Per-residue confidence metric (0-100). Higher values indicate more confident predictions.

PAE (Predicted Aligned Error): Matrix indicating confidence in relative positions between residue pairs. Low values (<5 Å) suggest confident relative positioning.

Database Version: Current version is v4. File URLs include version suffix (e.g., model_v4.cif).

Fragment Number: Large proteins may be split into fragments. Fragment number appears in AlphaFold ID (e.g., F1, F2).

Confidence Interpretation Guidelines

pLDDT Thresholds:

• >90: Very high confidence - suitable for detailed analysis
• 70-90: High confidence - generally reliable backbone structure
• 50-70: Low confidence - use with caution, flexible regions
• <50: Very low confidence - likely disordered or unreliable

PAE Guidelines:

• <5 Å: Confident relative positioning of domains
• 5-10 Å: Moderate confidence in arrangement
• >15 Å: Uncertain relative positions, domains may be mobile

Resources

references/api_reference.md

Comprehensive API documentation covering:

• Complete REST API endpoint specifications
• File format details and data schemas
• Google Cloud dataset structure and access patterns
• Advanced query examples and batch processing strategies
• Rate limiting, caching, and best practices
• Troubleshooting common issues

Consult this reference for detailed API information, bulk download strategies, or when working with large-scale datasets.

Important Notes

Data Usage and Attribution

• AlphaFold DB is freely available under CC-BY-4.0 license
• Cite: Jumper et al. (2021) Nature and Varadi et al. (2022) Nucleic Acids Research
• Predictions are computational models, not experimental structures
• Always assess confidence metrics before downstream analysis

Version Management

• Current database version: v4 (as of 2024-2025)
• File URLs include version suffix (e.g., _v4.cif)
• Check for database updates regularly
• Older versions may be deprecated over time

Data Quality Considerations

• High pLDDT doesn't guarantee functional accuracy
• Low confidence regions may be disordered in vivo
• PAE indicates relative domain confidence, not absolute positioning
• Predictions lack ligands, post-translational modifications, and cofactors
• Multi-chain complexes are not predicted (single chains only)

Performance Tips

• Use Biopython for simple single-protein access
• Use Google Cloud for bulk downloads (much faster than individual files)
• Cache downloaded files locally to avoid repeated downloads
• BigQuery free tier: 1 TB processed data per month
• Consider network bandwidth for large-scale downloads

Additional Resources

• AlphaFold DB Website: https://alphafold.ebi.ac.uk/
• API Documentation: https://alphafold.ebi.ac.uk/api-docs
• Google Cloud Dataset: https://cloud.google.com/blog/products/ai-machine-learning/alphafold-protein-structure-database
• 3D-Beacons API: https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/
• AlphaFold Papers:
  • Nature (2021): https://doi.org/10.1038/s41586-021-03819-2
  • Nucleic Acids Research (2024): https://doi.org/10.1093/nar/gkad1011
• Biopython Documentation: https://biopython.org/docs/dev/api/Bio.PDB.alphafold_db.html
• GitHub Repository: https://github.com/google-deepmind/alphafold