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I'm finding a web server (or standalone program) that allows the upload of a custom PDB for protein fold topology search.

Do you know any of them?

More details:

Actually I started off with Foldseek but have a question in mind:

how do I know if I have a novel fold? (because similarity search will often return partially similar hits).

Then, I tried to think of topology, as an illustration:

enter image description here

which simplifies structures to spatial arrangements of secondary structures (or topology).

I want to know if there's any database of protein fold topologies and tools for topology similarity search.

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  • $\begingroup$ Have you tried foldseek? $\endgroup$
    – user172818
    Commented May 9, 2023 at 0:18
  • $\begingroup$ I started off with foldseek but I need lower resolution search. $\endgroup$
    – Johnny Tam
    Commented May 9, 2023 at 10:55

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There are a few, but the main candidates for this would be :

  1. CATH - http://www.cathdb.info/
  2. SCOP - https://scop.mrc-lmb.cam.ac.uk/
  3. Ptgl - http://ptgl.uni-frankfurt.de/

CATH and Ptgl have search services on their website, but not sure about SCOP.

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