19Prefer the URLs returned by `/prediction/{uniprot_accession}` (`pdbUrl`, `cifUrl`, `bcifUrl`, `paeDocUrl`, `msaUrl`, `plddtDocUrl`, and AlphaMissense annotation URLs) instead of hardcoding a version. AlphaFold DB file names are versioned; as of the checked API response for `P00533`, `latestVersion` is `6`.

21Current direct-download patterns:

22```

23https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.pdb

24https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.cif

25https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.bcif

26https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-predicted_aligned_error_v6.json

27https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-confidence_v6.json

28https://alphafold.ebi.ac.uk/files/msa/AF-{UNIPROT}-F1-msa_v6.a3m

29```

Structure File URLs (direct download)

Prefer the URLs returned by /prediction/{uniprot_accession} (pdbUrl, cifUrl, bcifUrl, paeDocUrl, msaUrl, plddtDocUrl, and AlphaMissense annotation URLs) instead of hardcoding a version. AlphaFold DB file names are versioned; as of the checked API response for P00533, latestVersion is 6.

Current direct-download patterns:

https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.pdb
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.cif
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.bcif
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-predicted_aligned_error_v6.json
https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-confidence_v6.json
https://alphafold.ebi.ac.uk/files/msa/AF-{UNIPROT}-F1-msa_v6.a3m

Raw lines 17 to 30

31## Example Calls

32```

33# Get prediction metadata for EGFR

34https://alphafold.ebi.ac.uk/api/prediction/P00533

36# Download PDB or mmCIF structure from current metadata

37https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.pdb

38https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.cif

40# Download PAE (predicted aligned error)

41https://alphafold.ebi.ac.uk/files/AF-P00533-F1-predicted_aligned_error_v6.json

42```

Example Calls

# Get prediction metadata for EGFR
https://alphafold.ebi.ac.uk/api/prediction/P00533

# Download PDB or mmCIF structure from current metadata
https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.pdb
https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.cif

# Download PAE (predicted aligned error)
https://alphafold.ebi.ac.uk/files/AF-P00533-F1-predicted_aligned_error_v6.json

Raw lines 31 to 43

44## Response Format

45`/prediction/{accession}` returns a JSON array. Key fields include `modelEntityId`, `latestVersion`, `allVersions`, `globalMetricValue` (mean pLDDT), `sequenceStart`, `sequenceEnd`, `taxId`, `organismScientificName`, `pdbUrl`, `cifUrl`, `bcifUrl`, `paeDocUrl`, `paeImageUrl`, `plddtDocUrl`, `msaUrl`, and AlphaMissense annotation URLs when available.

47Coordinate files are available as PDB, mmCIF, and binary CIF. Prefer mmCIF/BCIF for large structures. Per-residue confidence is stored in the coordinate file B-factor column and is also available as confidence JSON. PAE is JSON.

49A single accession can return multiple isoforms as well as fragments: the 2026-09-30 `P04637` response returned nine model entities. Select the intended isoform and residue interval, and retain `modelEntityId`; do not silently take the first array element.

51Proteins longer than the model size limit may be represented as overlapping fragments (`F1`, `F2`, ...). Preserve fragment identifiers and residue ranges when reporting results.

Response Format

/prediction/{accession} returns a JSON array. Key fields include modelEntityId, latestVersion, allVersions, globalMetricValue (mean pLDDT), sequenceStart, sequenceEnd, taxId, organismScientificName, pdbUrl, cifUrl, bcifUrl, paeDocUrl, paeImageUrl, plddtDocUrl, msaUrl, and AlphaMissense annotation URLs when available.

Coordinate files are available as PDB, mmCIF, and binary CIF. Prefer mmCIF/BCIF for large structures. Per-residue confidence is stored in the coordinate file B-factor column and is also available as confidence JSON. PAE is JSON.

A single accession can return multiple isoforms as well as fragments: the 2026-09-30 P04637 response returned nine model entities. Select the intended isoform and residue interval, and retain modelEntityId; do not silently take the first array element.

Proteins longer than the model size limit may be represented as overlapping fragments (F1, F2, ...). Preserve fragment identifiers and residue ranges when reporting results.

Raw lines 44 to 52

53## Rate Limits

54No strict per-request limit is published. For many proteins, use the metadata endpoint to retrieve current URLs and pace requests conservatively. For proteome-scale or all-database retrievals, use AlphaFold DB's FTP/download pages or Google Cloud public dataset instead of looping over individual file URLs. The database contains over 200M monomer predictions, and current downloads also include selected AlphaFold complex predictions.

Rate Limits

No strict per-request limit is published. For many proteins, use the metadata endpoint to retrieve current URLs and pace requests conservatively. For proteome-scale or all-database retrievals, use AlphaFold DB's FTP/download pages or Google Cloud public dataset instead of looping over individual file URLs. The database contains over 200M monomer predictions, and current downloads also include selected AlphaFold complex predictions.

Raw lines 53 to 54