tools-only AlphaFold Predictions - Usage Guide
Overview
Download and analyze AI-predicted protein structures from the AlphaFold database, including confidence scores (pLDDT) and predicted aligned error (PAE) for assessing prediction quality.
Prerequisites
pip install biopython requests numpy
Quick Start
Tell your AI agent what you want to do:
- "Download the AlphaFold structure for UniProt P04637"
- "Check the confidence scores for this AlphaFold prediction"
- "Identify low-confidence regions in this predicted structure"
Example Prompts
Downloading Structures
"Download the AlphaFold model for UniProt ID P53_HUMAN"
"Get the AlphaFold structure for P04637 in mmCIF format"
"Fetch AlphaFold predictions for these 5 UniProt IDs"
Analyzing Confidence
"Show me the pLDDT scores for this AlphaFold structure"
"Which regions have low confidence (pLDDT < 70)?"
"Plot the per-residue confidence scores"
PAE Analysis
"Download and visualize the PAE matrix for this protein"
"Identify domain boundaries from the PAE data"
"Which domain-domain interactions are reliable?"
Quality Assessment
"Compare this AlphaFold prediction with the experimental structure"
"Highlight the confident vs disordered regions"
"Is this prediction reliable enough for docking?"
What the Agent Will Do
- Construct the AlphaFold database URL from UniProt ID
- Download the structure file (PDB or mmCIF format)
- Parse confidence scores from B-factor column (pLDDT)
- Optionally fetch PAE matrix for inter-residue error estimates
- Analyze and report on prediction quality
Database Access
Direct download URLs:
- Structure:
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-model_v4.pdb - mmCIF:
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-model_v4.cif - PAE:
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-predicted_aligned_error_v4.json
API endpoint: https://alphafold.ebi.ac.uk/api/prediction/{UNIPROT_ID}
Confidence Score Interpretation
| pLDDT Range | Interpretation | Color (AlphaFold DB) |
|---|---|---|
| 90-100 | Very high confidence | Blue |
| 70-90 | Confident | Cyan |
| 50-70 | Low confidence | Yellow |
| <50 | Very low (likely disordered) | Orange |
Tips
- Check pLDDT before using - Regions with pLDDT < 70 should be treated cautiously
- Use PAE for domains - Low PAE between residues indicates reliable relative positioning
- B-factor column holds pLDDT - Parse with Bio.PDB and read
atom.bfactor - Single conformation only - AlphaFold predicts one state, not conformational ensembles
- Compare when possible - Validate against experimental structures if available
- 200M+ structures available - Coverage includes most UniProt sequences