# AlphaFold Protein Structure Database License: permissive (CC-BY-4.0); Mdexa hosting: link-only. first-hand data-scope statement(s) allow commercial use and redistribution Risk flag(s): derived, model-generated. - Commercial use: Yes · Derivatives: Yes · Redistribution: Yes · File on Mdexa: No - License status: Permissive (CC-BY-4.0) - Mdexa hosting: Link only — License permissive: first-hand data-scope statement(s) allow commercial use and redistribution. Risk flag(s): derived, Model-generated. Link only. - Source risk: Derived, Model-generated - Last verified: 2026-11-14 - Card: https://mdexa.com/datasets/alphafold-db/ ## Key facts - Domain: Genomics and omics - Content type: Databases - Size: — — over 260 million protein structure predictions - Language: English - Modality: Text - Publisher: Google DeepMind and EMBL-EBI - Year: — ## Commercial use of AlphaFold Protein Structure Database - Commercial use: Yes. - License status: Permissive. - Conditions: Attribution Verdicts record what sources state and are not legal advice. ## AlphaFold Protein Structure Database license evidence first-hand data-scope statement(s) allow commercial use and redistribution - **Dataset page** — CC-BY-4.0: Statement found in snapshot s01 (page) — "Data is available for academic and commercial use, under a CC-BY-4.0 licence." — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (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." — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (page) — "AlphaFold Data Copyright (2022) DeepMind Technologies Limited." — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (page) — "Kinetoplastid data copyright (2025) Wheeler Lab" — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (page) — "AllTheBacteria data copyright (2025) AllTheBacteria Consortium" — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (page) — "A BFVD Data Copyright (2025) The BFVD Development Team" — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Dataset page**: Statement found in snapshot s01 (page) — "AlphaMissense Copyright (2023) DeepMind Technologies Limited." — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) - **Website footer**: Statement found in snapshot s01 (page) — "Copyright © EMBL 2023 EMBL-EBI is part of the European Molecular Biology Laboratory Terms of use" — https://alphafold.ebi.ac.uk/ (2026-11-12; Page opened) ## Source and lineage — - Derived from: UniProt - Derived from: PDB ## Known issues with AlphaFold Protein Structure Database — ## Preflight Not run (data not ingested). ## Downloading AlphaFold Protein Structure Database and API access Mdexa does not serve files. Original source: - https://alphafold.ebi.ac.uk/ - https://alphafold.ebi.ac.uk/faq ## Citing AlphaFold Protein Structure Database No recommended citation text. ## Machine-readable - JSON: https://mdexa.com/datasets/alphafold-db.json - 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). ## 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 DB provides open access to over 260 million protein structure predictions to accelerate scientific research. https://alphafold.ebi.ac.uk/ (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. > 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/ (2026-11-12) - The changelog entry dated 2025-09-15 states 241,070,489 structures. > 241,070,489 structures https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (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. > 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/ (2026-11-12) ### Identifiers - The README lists an AlphaFold DB identifier column with the example AF-A8H2R3-F1. > AlphaFold DB identifier, e.g. AF-A8H2R3-F1 https://ftp.ebi.ac.uk/pub/databases/alphafold/README.txt (2026-11-13) - The README's FASTA identifier row includes UA=UniprotAccession and UI=UniprotIdentifier fields. > >AFDB:UniqueIdentifier ProteinName UA=UniprotAccession UI=UniprotIdentifier https://ftp.ebi.ac.uk/pub/databases/alphafold/README.txt (2026-11-13) ### Access - Bulk download: http://ftp.ebi.ac.uk/pub/databases/alphafold/ - Web interface only: https://pmc.ncbi.nlm.nih.gov/articles/PMC10767828/ ### Versions - The latest dated entry in the changelog is 2025-09-15. > ## 2025-09-15 https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-13) - The changelog states that the CIF _database_2.database_id value changed from AF to AlphaFoldDB. > CIF: Updated `_database_2.database_id` from `AF` to `AlphaFoldDB` https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-13) - The changelog states that all CIF files are now ModelCIF-compliant. > All CIF files are now ModelCIF-compliant https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-13) - The changelog states that accession_ids.txt was renamed to accession_ids.csv. > FTP: Renamed accession_ids.txt to accession_ids.csv. https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-13) - The changelog lists a removed count of 39,324,993. > Removed: 39,324,993 https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-13) - In the 2025-09-15 release the mmCIF global pLDDT field was changed to a per-residue average instead of a per-atom average. > * CIF: Fixed global pLDDT `_ma_qa_metric_global.metric_value` to be computed as https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-14) - In 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. > * Structures with consecutive CA-CA distance > 10 A are now filtered out. https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-14) - In the 2022-07-28 release all CIF files became ModelCIF-compliant and the PAE file format changed. > * All CIF files are now ModelCIF-compliant https://ftp.ebi.ac.uk/pub/databases/alphafold/CHANGELOG.txt (2026-11-14) ### Suited for - The page states support for research into resistance mechanisms and new antimicrobial strategies. > Supports research into resistance mechanisms and new antimicrobial strategies. https://alphafold.ebi.ac.uk/ (2026-11-12) - The page states support for research on pathogens of major global public health importance. > Supports research on pathogens of major global public health importance. https://alphafold.ebi.ac.uk/ (2026-11-12) - Terwilliger et al. suggest treating AlphaFold predictions as hypotheses that accelerate but do not replace experimental structure determination. > We suggest considering AlphaFold predictions as exceptionally useful hypotheses. https://pmc.ncbi.nlm.nih.gov/articles/PMC10776388/ (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. > 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/ (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. > 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/ (2026-11-12) ### No sourced statement yet Update cycle, Known defects and misuse, Commercial licensing ## Continue in this database This record is one of 109 processed and verified records (datasets, data resources and open models). To find others, call `https://mcp.mdexa.com/v1/datasets?q=` or connect the MCP server at `https://mcp.mdexa.com/mcp`; no key is needed for 20 calls per minute. Rows are under 1 KB; an empty result means "not listed". For a list of items, one batch check (free account) returns a report. Guide: /agents.md. Similar records: ClinPGx/PharmGKB (https://mdexa.com/datasets/pharmgkb/); GEO (https://mdexa.com/datasets/geo/); gnomAD (https://mdexa.com/datasets/gnomad/).