| name | alphafold-db |
| description | Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession. |
| license | MIT |
| author | AIPOCH |
Source: https://github.com/aipoch/medical-research-skills
AlphaFold Database Skill
When to Use
- You have a UniProt accession (e.g.,
P00520) and need to download its AlphaFold-predicted 3D structure in mmCIF or PDB format.
- You want to assess prediction reliability using per-residue pLDDT confidence scores.
- You need PAE (Predicted Aligned Error) data to support domain-level interpretation or inter-domain confidence checks.
- You want to programmatically retrieve AlphaFold DB metadata (e.g., model/structure URLs and related fields) for downstream pipelines.
- You are building an automated workflow that fetches structures + confidence metrics for many proteins by UniProt ID.
Key Features
- Fetch AlphaFold DB predicted structures by UniProt accession.
- Download structure files in mmCIF (default) or PDB.
- Retrieve and save metadata JSON, including confidence-related fields (e.g., pLDDT) and URL information.
- Simple CLI workflow suitable for scripting and batch processing.
Dependencies
- Python
>=3.8
requests >=2.25
Example Usage
Fetch the structure and metadata for a UniProt ID and save them to a directory:
python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format cif
Fetch as PDB instead:
python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format pdb
Expected outputs in ./out:
P00520.cif (or P00520.pdb)P00520_metadata.json (includes confidence/URL fields such as pLDDT-related information)
Implementation Details
- Input identifier: UniProt accession ID (e.g.,
P00520).
- Formats:
--format cif (default): downloads an mmCIF structure file.--format pdb: downloads a PDB structure file.
- Artifacts written:
- Structure file named
<UNIPROT_ID>.<cif|pdb>.
- Metadata JSON named
<UNIPROT_ID>_metadata.json, used to store confidence metrics (e.g., pLDDT) and AlphaFold DB URL-related fields.
- API reference: Endpoint and response details are documented in
references/api_reference.md.
