Agent skill

bio-structural-biology-alphafold-predictions

Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

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Install this agent skill to your Project

npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-structural-biology-alphafold-predictions

SKILL.md

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

python
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

python
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')

Get Metadata

python
def get_alphafold_info(uniprot_id):
    '''Get AlphaFold prediction metadata'''
    url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}'
    response = requests.get(url)
    if response.status_code == 200:
        return response.json()[0]
    return None

info = get_alphafold_info('P04637')
print(f"Gene: {info['gene']}")
print(f"Organism: {info['organismScientificName']}")
print(f"Model version: {info['latestVersion']}")

File Types Available

Database version v4 (current as of 2025). The version number refers to the database release, not the AlphaFold model version.

File URL Pattern Description
PDB AF-{id}-F1-model_v4.pdb Structure coordinates
mmCIF AF-{id}-F1-model_v4.cif Structure with metadata
PAE JSON AF-{id}-F1-predicted_aligned_error_v4.json Predicted aligned error
python
def download_pae(uniprot_id, output_dir='.'):
    '''Download PAE (predicted aligned error) matrix'''
    url = f'https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-predicted_aligned_error_v4.json'
    response = requests.get(url)
    if response.status_code == 200:
        output_path = f'{output_dir}/AF-{uniprot_id}-F1-pae.json'
        with open(output_path, 'w') as f:
            f.write(response.text)
        return output_path
    return None

Analyze pLDDT Confidence Scores

Extract from PDB B-factors

AlphaFold stores pLDDT scores in the B-factor column.

python
from Bio.PDB import PDBParser

def extract_plddt(pdb_file):
    '''Extract pLDDT confidence scores from AlphaFold PDB'''
    parser = PDBParser(QUIET=True)
    structure = parser.get_structure('protein', pdb_file)

    residue_plddt = {}
    for model in structure:
        for chain in model:
            for residue in chain:
                if residue.id[0] == ' ':  # Standard residue
                    ca = residue['CA'] if 'CA' in residue else list(residue.get_atoms())[0]
                    residue_plddt[residue.id[1]] = ca.get_bfactor()
    return residue_plddt

plddt = extract_plddt('AF-P04637-F1-model_v4.pdb')
avg_plddt = sum(plddt.values()) / len(plddt)
print(f'Average pLDDT: {avg_plddt:.1f}')

Confidence Interpretation

pLDDT Confidence Interpretation
>90 Very high High accuracy, can be used as experimental
70-90 Confident Good backbone, may have sidechain errors
50-70 Low Caution, may be disordered
<50 Very low Likely disordered or wrong

Plot pLDDT per Residue

python
import matplotlib.pyplot as plt

def plot_plddt(plddt_dict, output='plddt_plot.png'):
    residues = sorted(plddt_dict.keys())
    scores = [plddt_dict[r] for r in residues]

    plt.figure(figsize=(12, 4))
    plt.fill_between(residues, scores, alpha=0.3)
    plt.plot(residues, scores)
    plt.axhline(y=70, color='orange', linestyle='--', label='Confident threshold')
    plt.axhline(y=90, color='green', linestyle='--', label='Very high threshold')
    plt.xlabel('Residue')
    plt.ylabel('pLDDT')
    plt.ylim(0, 100)
    plt.legend()
    plt.savefig(output)
    plt.close()

plot_plddt(plddt)

Analyze PAE (Predicted Aligned Error)

python
import json
import numpy as np
import matplotlib.pyplot as plt

def load_pae(pae_file):
    '''Load PAE matrix from JSON'''
    with open(pae_file) as f:
        data = json.load(f)

    # AlphaFold v4 format
    if 'predicted_aligned_error' in data[0]:
        return np.array(data[0]['predicted_aligned_error'])
    # Older format
    return np.array(data['predicted_aligned_error'])

def plot_pae(pae_matrix, output='pae_plot.png'):
    plt.figure(figsize=(8, 8))
    plt.imshow(pae_matrix, cmap='Greens_r', vmin=0, vmax=30)
    plt.colorbar(label='Expected position error (A)')
    plt.xlabel('Scored residue')
    plt.ylabel('Aligned residue')
    plt.title('Predicted Aligned Error')
    plt.savefig(output)
    plt.close()

pae = load_pae('AF-P04637-F1-pae.json')
plot_pae(pae)

PAE Interpretation

  • Low PAE (green): Residues have well-defined relative positions
  • High PAE (white): Uncertain relative positions (flexible linkers, domains)
  • Diagonal blocks: Distinct structural domains

Batch Download

python
def batch_download_alphafold(uniprot_ids, output_dir='.'):
    '''Download multiple AlphaFold structures'''
    import os
    os.makedirs(output_dir, exist_ok=True)

    results = {}
    for uid in uniprot_ids:
        pdb_file = download_alphafold(uid, output_dir)
        results[uid] = pdb_file
        if pdb_file:
            print(f'Downloaded: {uid}')
        else:
            print(f'Not found: {uid}')
    return results

ids = ['P04637', 'P53_HUMAN', 'Q9Y6K9']
files = batch_download_alphafold(ids, 'alphafold_structures')

Compare with Experimental Structure

python
from Bio.PDB import PDBParser, Superimposer

def compare_structures(alphafold_pdb, experimental_pdb):
    '''Calculate RMSD between AlphaFold and experimental structure'''
    parser = PDBParser(QUIET=True)
    af_struct = parser.get_structure('af', alphafold_pdb)
    exp_struct = parser.get_structure('exp', experimental_pdb)

    # Get CA atoms from first chain
    af_atoms = [r['CA'] for r in af_struct[0].get_residues() if 'CA' in r]
    exp_atoms = [r['CA'] for r in exp_struct[0].get_residues() if 'CA' in r]

    # Align by length (simple approach)
    min_len = min(len(af_atoms), len(exp_atoms))
    af_atoms = af_atoms[:min_len]
    exp_atoms = exp_atoms[:min_len]

    super_imposer = Superimposer()
    super_imposer.set_atoms(exp_atoms, af_atoms)
    rmsd = super_imposer.rms
    return rmsd

Related Skills

  • structural-biology/structure-io - Load and parse PDB/mmCIF files
  • structural-biology/geometric-analysis - RMSD, superimposition
  • database-access/uniprot-access - Get UniProt IDs for proteins
  • structural-biology/structure-navigation - Navigate structure hierarchy

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