Version Compatibility

Reference examples tested with: BioPython 1.83+, matplotlib 3.8+, numpy 1.26+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

AlphaFold Predictions

"Get the AlphaFold predicted structure for my protein" → Download pre-computed AlphaFold structures by UniProt ID and assess prediction quality via per-residue pLDDT confidence scores.

• Python: requests.get(f'https://alphafold.ebi.ac.uk/files/AF-{uniprot}-F1-model_v4.pdb')

Download and analyze AlphaFold predicted protein structures from the AlphaFold Protein Structure Database.

Download Structures

Goal: Retrieve pre-computed AlphaFold protein structure predictions and assess prediction quality via pLDDT confidence scores.

Approach: Query the AlphaFold Protein Structure Database API by UniProt accession to download PDB/CIF files, then extract per-residue pLDDT scores from B-factor columns to identify high-confidence and disordered regions.

Single Structure by UniProt ID

import requests

def download_alphafold(uniprot_id, output_dir='.'):
    '''Download AlphaFold structure for UniProt accession'''
    base_url = 'https://alphafold.ebi.ac.uk/files'
    pdb_url = f'{base_url}/AF-{uniprot_id}-F1-model_v4.pdb'
    cif_url = f'{base_url}/AF-{uniprot_id}-F1-model_v4.cif'

    response = requests.get(pdb_url)
    if response.status_code == 200:
        output_path = f'{output_dir}/AF-{uniprot_id}-F1-model_v4.pdb'
        with open(output_path, 'w') as f:
            f.write(response.text)
        return output_path
    return None

pdb_file = download_alphafold('P04637')  # Human p53

Check Availability

def check_alphafold_exists(uniprot_id):
    '''Check if AlphaFold prediction exists'''
    url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}'
    response = requests.get(url)
    return response.status_code == 200

if check_alphafold_exists('P04637'):
    print('AlphaFold structure available')