Some previously accessible protein IDs are no longer searchable in the AlphaFold database

[lh12565]

Hi, I am writing to report an issue regarding the search functionality of the AlphaFold database at https://alphafold.ebi.ac.uk/. I have noticed that certain protein IDs (such as Q01628) that were previously searchable and from which I successfully downloaded predicted structures can no longer be found via the search box on the website.

My main questions are:

1. What are the primary reasons that could cause specific protein entries to become unavailable for search in the database?

2. Are the previously downloaded PDB/CIF prediction files for these IDs still valid and suitable for continued analysis, even if the entry is no longer listed online?

Thanks!

[CodeVishal-17]

Thanks for reporting this — this seems consistent with UniProt ID remapping or AlphaFold DB re-indexing rather than model invalidation.

In similar cases, the underlying structure files remain valid, but the search index no longer exposes deprecated or merged UniProt accessions.

It might be helpful to clarify:

• whether these IDs were deprecated/merged upstream in UniProt
• and whether direct URL access or archived mappings still exist for such entries

Happy to help test or verify with additional examples if needed.

[lh12565]

Thanks for reporting this — this seems consistent with UniProt ID remapping or AlphaFold DB re-indexing rather than model invalidation.

In similar cases, the underlying structure files remain valid, but the search index no longer exposes deprecated or merged UniProt accessions.

It might be helpful to clarify:

• whether these IDs were deprecated/merged upstream in UniProt
• and whether direct URL access or archived mappings still exist for such entries

Happy to help test or verify with additional examples if needed.

Thank you for the guidance. However, the protein ID Q01628 is still active in UniProt, you can view the current entry here: https://www.uniprot.org/uniprotkb/Q01628/entry. I tried to access the structure directly via https://alphafold.ebi.ac.uk/entry/Q01628. However, it now returns a “No entry found” error page. I distinctly remember being able to access this exact URL in the past and successfully downloaded the predicted structure file from it.
Since Q01628 remains a valid UniProt accession (not deprecated or merged), its disappearance from the AlphaFold database search seems less likely to be due to an upstream ID change.
Thank you again for your time and support.

[ionfwsrijan]

Hi there,

I’m Srijan Jaiswal, and I’m eager to contribute to this project as part of my open-source contribution. I have reviewed this issue and feel confident that I can provide a solution since I have experience working with similar technologies in my past projects. Could you please assign this issue to me? I’d love to work on it and contribute to the project.

Best regards,
Srijan Jaiswal