Query on Using BFVD CIF Files as Templates for AlphaFold/ColabFold

[mohmhm1]

Hello,

I’m exploring the possibility of using BFVD as a template database for AlphaFold/ColabFold predictions and wanted to ask if there has been any effort or discussion on this integration.

Specifically, when I use a BFVD-converted CIF file as a template, I encounter the following error in AlphaFold:
  “No protein chains found in this file”

From what I understand, the AlphaFold mmCIF parser (in the _get_protein_chains() function) expects the CIF file to include an _entity_poly_seq loop with fields such as _entity_poly_seq.entity_id, _entity_poly_seq.mon_id, and _entity_poly_seq.num. It seems that the current BFVD CIF conversion might not be adding these fields, which prevents the templates from being recognized properly.

I’d like to know if:
1. There has been any previous effort to use BFVD as a template database for AlphaFold,
2. You have any plans to adjust the conversion process to include the required _entity_poly_seq loop (or similar metadata) for better compatibility with AlphaFold/ColabFold template parsing.

Thank you for your time and for your excellent work on BFVD!

[rachelse]

Hello,

Sorry for late response and thank you for your attempt to use BFVD as templates. We are planning to release updated BFVD within next week, accompanying the CIF files update. I hope the update can solve your issue.

To answer your questions,

1. So far, we never heard about the trial. But, we hope more people can utilize BFVD as template for viral predictions.
2. We advanced the CIF files a bit, including the elements you'd mentioned. I'll once reply again here once we update BFVD. Please let us know if the updated CIF files still have the issue.

[mohmhm1]

Hi thank you for your response. Any updates on the updated BFVD yet?

[rachelse]

Sorry for being delayed. We just updated our database with new version!

With new cif files, we included the elements you'd mentioned. You can find the cif files here.

Please let us know if those cif files having troubles while serving as templates.
Thank you!