FoldSeek Behavior with PolyGLY Backbone Structures

[SarahKnapp1]

Hello,

I recently ran a backbone structure containing PolyGLY through the FoldSeek server and received zero hits. However, when I used the same fold with side chains (generated via AlphaFold) and subsequently removed the side chains, I obtained many results.

I was wondering if there is a specific reason why PolyGLY structures are not yielding results, or if this might be a technical issue with the server.

Thank you!
Sarah Knapp

[milot-mirdita]

Can you share the structure? Then we can take a look why it doesn't yield any hits.

[SarahKnapp1]

Attaching the structures. I was unable to upload a .PDB file, so I converted them to .txt instead. [refoldAF_without_sidechains.txt](https://github.com/user-attachments/files/18480752/refoldAF_without_sidechains.txt) [RFdiffusion_polyGLY.txt](https://github.com/user-attachments/files/18480751/RFdiffusion_polyGLY.txt) Thanks for your fast response.

[milot-mirdita]

I think you have to upload them through the github interface

[martin-steinegger]

I just try to search it on the webserver, the version without sidechains find more hits.
refoldAF_without_sidechains.txt webserver: https://search.foldseek.com/result/t4JkopvHffykMdlyRu8pXlgjkhl1CjfrpseKiw/0
RFdiffusion_polyGLY.txt webserver: https://search.foldseek.com/result/Mrghyu7qrhm-GCeTBC0xPm77ZD6yr39v9ykU7w/0

[milot-mirdita]

We don't expose the option in the webserver, but you could also try a search with the 3Di only scoring mode --alignment-type 0 with a local foldseek installation. That should better with a GLY-only structure.

[SarahKnapp1]

I just try to search it on the webserver, the version without sidechains find more hits. refoldAF_without_sidechains.txt webserver: https://search.foldseek.com/result/t4JkopvHffykMdlyRu8pXlgjkhl1CjfrpseKiw/0 RFdiffusion_polyGLY.txt webserver: https://search.foldseek.com/result/Mrghyu7qrhm-GCeTBC0xPm77ZD6yr39v9ykU7w/0

Thank you so much!
When I run the RFdiffusion_polyGLY.txt I get no hits: https://search.foldseek.com/result/5tziu3mJVQ9JWPHae5An5XIARrews8Ycpd1d7w/0

[SarahKnapp1]

We don't expose the option in the webserver, but you could also try a search with the 3Di only scoring mode --alignment-type 0 with a local foldseek installation. That should better with a GLY-only structure.

Thank you so much! I will try it out.