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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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Back Translate 3Di Tokesn to PDB Format #225

Closed mahdip72 closed 3 months ago

mahdip72 commented 8 months ago

Hello, I have a few questions which might be very basic to others.

  1. Can we convert the 3Di tokens produced by foldseek into the actual 3D structure format like PDB files?

  2. How can I compare two sequences of predicted and true 3Di tokens? Can I use something like the TM Score for that? I am working on a model to predict 3Di tokens from amino acids and am searching for the best metric to evaluate the model.

I would be very greatful to whom can answer my questions.

Leo-T-Zang commented 3 months ago

https://github.com/steineggerlab/foldseek/issues/273