AlphaFold Database

What It Does

• Provides predicted 3D protein structures for nearly every known protein
• Per-residue confidence scores (pLDDT 0-100): >90 high confidence, 70-90 good, 50-70 low, <50 disordered
• Predicted Aligned Error (PAE) for domain-level confidence
• Downloadable PDB/mmCIF files

How to Use

### Web Interface

1. Go to https://alphafold.ebi.ac.uk

2. Search by UniProt ID (e.g., Q7RTU9 for STRC) or gene name

3. View 3D structure colored by pLDDT confidence

4. Download structure files

### API (Programmatic)

        # Get structure by UniProt ID
        curl https://alphafold.ebi.ac.uk/api/prediction/Q7RTU9
        
        # Download PDB file
        curl -O https://alphafold.ebi.ac.uk/files/AF-Q7RTU9-F1-model_v4.pdb
        

### Python

        import requests
        r = requests.get("https://alphafold.ebi.ac.uk/api/prediction/Q7RTU9")
        data = r.json()[0]
        print(f"pLDDT: {data['globalMetricValue']}")
        print(f"PDB URL: {data['pdbUrl']}")
        

Verified Status

VERIFIED — STRC (Q7RTU9) structure available (model v6). pLDDT at E1659: 95.69/100 — very high confidence, well-structured region. pLDDT profile shows high confidence in core domain (residues ~700-1775), low confidence in N-terminal disordered region.

STRC Research Usage

• STRC pLDDT Profile and Cut Point Analysis — used to identify mini-STRC truncation boundaries
• STRC ESMFold Disorder Validation — cross-validated disorder predictions
• Residue E1659 falls in a well-structured region (pLDDT >80)

Results (April 2026)

• PAE analysis DONE: E1659 has avg PAE 16.8Å (moderate), but 362 residues with PAE <5Å (confident interactions). 99 confident interactions within ±50 residues = E1659 is in a well-connected structural neighborhood.
• ESMFold comparison DONE: cross-validated in STRC ESMFold Disorder Validation
• Next: batch download ortholog structures, molecular dynamics

Results (April 2026)

• PAE analysis DONE: E1659 has avg PAE 16.8Å (moderate), but 362 residues with PAE <5Å (confident interactions). 99 confident interactions within ±50 residues = E1659 is in a well-connected structural neighborhood.
• ESMFold comparison DONE: cross-validated in STRC ESMFold Disorder Validation
• Next: batch download ortholog structures, molecular dynamics