AlphaFold Database Download

Fetch AlphaFold DB CIF, PDB, BCIF, and PAE JSON files from a UniProt accession.

Input

Entry ID

Database

Output format

Output

Configure inputs to begin

Set options on the left, then click “Fetch downloads” — or start from an example.

P00533

Q8W3K0

P69905

How to download AlphaFold DB structures?

AlphaFold Database Download fetches predicted structure files and confidence metadata from AlphaFold DB using a UniProt accession. It returns CIF, PDB, BCIF, and PAE JSON downloads when those files are available for the entry.

Use this tool when you need the AlphaFold DB model files for visualization, comparison, confidence analysis, or downstream structure processing.

Input	Description
`Entry ID`	UniProt accession. Examples: `P00533`, `Q8W3K0`, `P69905`.

Setting	Description
`Database`	Opens the selected database download tool.
`Output format`	Return all files, CIF, PDB, BCIF, or PAE JSON.

Supported AlphaFold DB downloads

File	Format	Use
CIF	`.cif`	Predicted structure in mmCIF format.
PDB	`.pdb`	Predicted structure in PDB format when provided.
BCIF	`.bcif`	Binary CIF structure file for efficient transfer.
PAE JSON	`.json`	Predicted aligned error data for confidence interpretation.

Understanding the results

The downloaded structure files contain the predicted coordinates for the selected UniProt accession. The PAE JSON file stores pairwise confidence information and is useful when judging domain placement or flexible regions.

Filenames follow the pattern:

Text

alphafold-P00533-cif.cif
alphafold-P00533-pdb.pdb
alphafold-P00533-bcif.bcif
alphafold-P00533-pae-json.json

For new predictions rather than database retrieval, use AlphaFold2, ESMFold, or Boltz-2.

Common use cases

Download an AlphaFold DB model for structure comparison.
Inspect predicted structures in PDB Viewer.
Pair coordinates with PAE JSON confidence data.
Retrieve predicted models before pocket or surface analysis.

FAQ

What identifier should I enter?

Enter the UniProt accession for the protein, such as P00533. Gene symbols are less reliable for direct AlphaFold DB downloads.

What is PAE JSON?

PAE means predicted aligned error. It estimates expected position error between residue pairs and helps identify confident domains and uncertain relative domain orientations.

Are these experimental structures?

No. AlphaFold DB entries are predicted structures. For experimental structures, use PDB Download or PDBe Download.

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