AlphaFold Protein Structure Database
Verified by Mdexa · Checked against the source text under public rules.How we check
- Commercial use
- Yes
- Derivatives
- Yes
- Redistribution
- Yes
- File on Mdexa
- NoLink only
first-hand data-scope statement(s) allow commercial use and redistribution
Cite this pageMdexa, AlphaFold Protein Structure Database, https://mdexa.com/datasets/alphafold-db/, verified 2026-11-14.
Source riskDerivedModel-generated
Key facts
- Domain
- Genomics and omics Modern medicine
- Content
- DatabasesOpen-access database of over 260 million AI-predicted protein structure entries developed by Google DeepMind and EMBL-EBI, with broad coverage of UniProt proteomes.
- Size
- —As stated: over 260 million protein structure predictions
- Language / modality
- English / Text
- Publisher
- Google DeepMind and EMBL-EBI
- Year
- —
- Expert review
- —
- Verification
- Verified: license text seen
Commercial use of AlphaFold Protein Structure Database
Commercial use: Yes. License status: Permissive.
- Conditions
- Attribution
Quoted statements and their sources are in AlphaFold Protein Structure Database license evidence.
Verdicts record what sources state and are not legal advice.
Practical information
Content scope
- The page states that AlphaFold DB provides open access to over 260 million protein structure predictions to accelerate scientific research.
alphafold.ebi.ac.uk ·
AlphaFold DB provides open access to over 260 million protein structure predictions to accelerate scientific research.
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
- The page states that the latest database release contains over 200 million entries and provides broad coverage of UniProt, the standard repository of protein sequences and annotations.
alphafold.ebi.ac.uk ·
The latest database release contains over 200 million entries, providing broad coverage of UniProt (the standard repository of protein sequences and annotations).
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
- The changelog entry dated 2025-09-15 states 241,070,489 structures.
ftp.ebi.ac.uk ·
241,070,489 structures
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- The page states that individual downloads are provided for the human proteome and for the proteomes of 47 other key organisms important in research and global health.
alphafold.ebi.ac.uk ·
We provide individual downloads for the human proteome and for the proteomes of 47 other key organisms important in research and global health.
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
Identifiers
- AlphaFold DB identifierThe README lists an AlphaFold DB identifier column with the example AF-A8H2R3-F1.
ftp.ebi.ac.uk ·
AlphaFold DB identifier, e.g. AF-A8H2R3-F1
https://ftp.ebi.ac.uk/pub/databases/alphafold/README.txt · README · checked 2026-11-13
- → UniProtThe README's FASTA identifier row includes UA=UniprotAccession and UI=UniprotIdentifier fields.
ftp.ebi.ac.uk ·
>AFDB:UniqueIdentifier ProteinName UA=UniprotAccession UI=UniprotIdentifier
https://ftp.ebi.ac.uk/pub/databases/alphafold/README.txt · README · checked 2026-11-13
Access
- Bulk downloadftp.ebi.ac.uk PDB · mmCIF
Same terms as the card's license.
- Web interface onlypmc.ncbi.nlm.nih.gov
Same terms as the card's license.
Versions
- LatestThe latest dated entry in the changelog is 2025-09-15.
ftp.ebi.ac.uk ·
## 2025-09-15
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- Breaking changeThe changelog states that the CIF _database_2.database_id value changed from AF to AlphaFoldDB.
ftp.ebi.ac.uk ·
CIF: Updated `_database_2.database_id` from `AF` to `AlphaFoldDB`
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- Breaking changeThe changelog states that all CIF files are now ModelCIF-compliant.
ftp.ebi.ac.uk ·
All CIF files are now ModelCIF-compliant
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- Breaking changeThe changelog states that accession_ids.txt was renamed to accession_ids.csv.
ftp.ebi.ac.uk ·
FTP: Renamed accession_ids.txt to accession_ids.csv.
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- Breaking changeThe changelog lists a removed count of 39,324,993.
ftp.ebi.ac.uk ·
Removed: 39,324,993
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · Dataset page · checked 2026-11-13
- Breaking changeIn the 2025-09-15 release the mmCIF global pLDDT field was changed to a per-residue average instead of a per-atom average.
ftp.ebi.ac.uk ·
* CIF: Fixed global pLDDT `_ma_qa_metric_global.metric_value` to be computed as
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · official-release-notes · checked 2026-11-14
- Breaking changeIn the 2022-11-01 (v4) release about 4.4% of predictions received updated coordinates, and structures with consecutive CA-CA distances above 10 Å were filtered out.
ftp.ebi.ac.uk ·
* Structures with consecutive CA-CA distance > 10 A are now filtered out.
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · official-release-notes · checked 2026-11-14
- Breaking changeIn the 2022-07-28 release all CIF files became ModelCIF-compliant and the PAE file format changed.
ftp.ebi.ac.uk ·
* All CIF files are now ModelCIF-compliant
https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt · official-release-notes · checked 2026-11-14
Suited for
- The page states support for research into resistance mechanisms and new antimicrobial strategies.
alphafold.ebi.ac.uk ·
Supports research into resistance mechanisms and new antimicrobial strategies.
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
- The page states support for research on pathogens of major global public health importance.
alphafold.ebi.ac.uk ·
Supports research on pathogens of major global public health importance.
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
- Terwilliger et al. suggest treating AlphaFold predictions as hypotheses that accelerate but do not replace experimental structure determination.
pmc.ncbi.nlm.nih.gov ·
We suggest considering AlphaFold predictions as exceptionally useful hypotheses.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10776388/ · peer-reviewed-paper · checked 2026-11-14
- AlphaFold DB states regions with pLDDT above 90 are generally modelled with high accuracy and suitable for applications such as characterising binding sites.
pmc.ncbi.nlm.nih.gov ·
Regions with pLDDT greater than 90 are generally modelled with high accuracy, making them suitable for high accuracy-dependent applications such as characterising binding sites.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10767828/ · peer-reviewed-paper · checked 2026-11-14
Not suited for
- The page states that if a use case is not covered by the database, users can generate their own AlphaFold predictions using the open source code.
alphafold.ebi.ac.uk ·
If your use case isn't covered by the database, you can generate your own AlphaFold predictions using this open source code
https://alphafold.ebi.ac.uk/ · Dataset page · checked 2026-11-12
AlphaFold Protein Structure Database license evidence 8
-
Dataset pagePage opened
CC-BY-4.0Third-party text · Dataset page
Data is available for academic and commercial use, under a CC-BY-4.0 licence.
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
EMBL-EBI expects attribution (e.g., in publications, services, or products) for any of its online services, databases, or software in accordance with good scientific practice.
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
AlphaFold Data Copyright (2022) DeepMind Technologies Limited.
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
Kinetoplastid data copyright (2025) Wheeler Lab
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
AllTheBacteria data copyright (2025) AllTheBacteria Consortium
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
A BFVD Data Copyright (2025) The BFVD Development Team
Statement found in snapshot s01 (page)
-
Dataset pagePage opened
Third-party text · Dataset page
AlphaMissense Copyright (2023) DeepMind Technologies Limited.
Statement found in snapshot s01 (page)
-
Website footerPage opened
Third-party text · Website footer
Copyright © EMBL 2023 EMBL-EBI is part of the European Molecular Biology Laboratory Terms of use
Statement found in snapshot s01 (page)
Source and lineage
- Derived fromUniProtnot in the database
- Derived fromPDBnot in the database
Known issues with AlphaFold Protein Structure Database
—
Preflight
Not run Runs only on ingested data; says nothing about quality.
Downloading AlphaFold Protein Structure Database and API access
No file on Mdexa (see the verdict). Get it from the source and confirm the terms there:
Citing AlphaFold Protein Structure Database
Mdexa, AlphaFold Protein Structure Database, https://mdexa.com/datasets/alphafold-db/, verified 2026-11-14.
More citation details
The source gives no citation text; the line above cites this card.
Machine-readable
alphafold-db.jsonalphafold-db.mdcatalog.json
Change log 8
| 2026-11-14 | Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. | |
| 2026-11-14 | Practical fields (scope, identifiers, access methods, versions, known defects) were added by the automated pipeline from stored page snapshots; every statement carries a verbatim quote. | |
| 2026-11-14 | Known defects, version notes and access statements from cited sources (papers, release notes, official pages) were added; each shows who said it, when, and what kind of source it is. | |
| 2026-11-14 | Re-adjudicated under the current rules; all machine checks still pass. | |
| 2026-11-14 | Re-adjudicated under the current rules; all machine checks still pass. | |
| 2026-11-13 | Re-adjudicated under the current rules; all machine checks still pass. | |
| 2026-11-13 | Re-adjudicated under the current rules; all machine checks still pass. | |
| 2026-11-13 | Added via the automated pipeline and passed all checks (gates, verbatim quotes, rule engine, two independent extractions). |
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