Download PDB, CIF, and FASTA files from RCSB PDB by 4-character structure ID.
Download PDBe structure files as PDB and CIF by PDB ID.
Download BindingDB binding record files by BindingDB monomer ID.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.
Download UniProt protein sequence records as FASTA and JSON by accession.
PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.
Convert Protein Data Bank files to Crystallographic Information File format
Download ChEBI chemical entity records as JSON by ChEBI ID.
Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.
Download PDB, CIF, and FASTA files from RCSB PDB by 4-character structure ID.
Download PDBe structure files as PDB and CIF by PDB ID.
Download BindingDB binding record files by BindingDB monomer ID.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.
Download UniProt protein sequence records as FASTA and JSON by accession.
PDBFixer is an OpenMM-based tool used for fixing problems in protein/DNA/RNA structure files, including adding missing atoms, adding missing residues, and fixing improper formatting.
Convert Protein Data Bank files to Crystallographic Information File format
Download ChEBI chemical entity records as JSON by ChEBI ID.
Download ChEMBL molecule records as JSON and SDF by ChEMBL compound ID.
Configure inputs to begin
Set options on the left, then click “Fetch downloads” — or start from an example.
P00533
Q8W3K0
P69905
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. |
| 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. |
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:
alphafold-P00533-cif.cif
alphafold-P00533-pdb.pdb
alphafold-P00533-bcif.bcif
alphafold-P00533-pae-json.jsonFor new predictions rather than database retrieval, use AlphaFold2, ESMFold, or Boltz-2.
Enter the UniProt accession for the protein, such as P00533. Gene symbols are less reliable for direct AlphaFold DB downloads.
PAE means predicted aligned error. It estimates expected position error between residue pairs and helps identify confident domains and uncertain relative domain orientations.
No. AlphaFold DB entries are predicted structures. For experimental structures, use PDB Download or PDBe Download.