66 lines
3.0 KiB
Markdown
66 lines
3.0 KiB
Markdown
---
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title: "AlphaFold DB (Predicted Protein Structures)"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e024ea8/skills/database-lookup/references/alphafold.md
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upstream_sha: 1e024ea8
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imported_at: 2026-07-02
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# AlphaFold DB (Predicted Protein Structures)
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## Base URL
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```
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https://alphafold.ebi.ac.uk/api/
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```
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## Auth
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No auth required.
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## Key Endpoints
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| Endpoint | Description |
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|----------|-------------|
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| `/prediction/{uniprot_accession}` | Prediction metadata and current file URLs by UniProt accession |
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## Structure File URLs (direct download)
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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`.
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Current direct-download patterns:
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```
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https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.pdb
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https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.cif
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https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-model_v6.bcif
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https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-predicted_aligned_error_v6.json
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https://alphafold.ebi.ac.uk/files/AF-{UNIPROT}-F1-confidence_v6.json
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https://alphafold.ebi.ac.uk/files/msa/AF-{UNIPROT}-F1-msa_v6.a3m
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```
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## Example Calls
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```
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# Get prediction metadata for EGFR
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https://alphafold.ebi.ac.uk/api/prediction/P00533
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# Download PDB or mmCIF structure from current metadata
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https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.pdb
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https://alphafold.ebi.ac.uk/files/AF-P00533-F1-model_v6.cif
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# Download PAE (predicted aligned error)
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https://alphafold.ebi.ac.uk/files/AF-P00533-F1-predicted_aligned_error_v6.json
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```
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## Response Format
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`/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.
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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.
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Proteins longer than the model size limit may be represented as overlapping fragments (`F1`, `F2`, ...). Preserve fragment identifiers and residue ranges when reporting results.
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## Rate Limits
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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.
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