Answers.Body: <p>There are a few, but the main candidates for this would be :</p>
  <ol>
  <li>CATH - <a href="http://www.cathdb.info/" rel="nofollow noreferrer">http://www.cathdb.info/</a></li>
  <li>SCOP - <a href="https://scop.mrc-lmb.cam.ac.uk/" rel="nofollow noreferrer">https://scop.mrc-lmb.cam.ac.uk/</a></li>
  <li>Ptgl - <a href="http://ptgl.uni-frankfurt.de/" rel="nofollow noreferrer">http://ptgl.uni-frankfurt.de/</a></li>
  </ol>
  <p>CATH and Ptgl have search services on their website, but not sure about SCOP.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-05-09T11:57:34.657Z
Answers.LastActivityDate: 2023-05-09T11:57:34.657Z
Answers.UserDisplayName: gilleain
Body: <p>I'm finding a web server (or standalone program) that allows the upload of a custom PDB for protein fold topology search.</p>
  <p>Do you know any of them?</p>
  <p>More details:</p>
  <p>Actually I started off with Foldseek but have a question in mind:</p>
  <p>how do I know if I have a novel fold? (because similarity search will often return partially similar hits).</p>
  <p>Then, I tried to think of topology, as an illustration:</p>
  <p><a href="https://i.sstatic.net/UE70k.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/UE70k.png" alt="enter image description here" /></a></p>
  <p>which simplifies structures to spatial arrangements of secondary structures (or topology).</p>
  <p>I want to know if there's any database of protein fold topologies and tools for topology similarity search.</p>
  <p>ADD COMMENT • link • edit •</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-09T00:18:26.653Z
Comments.Text: Have you tried [foldseek](https://search.foldseek.com/search)?
Comments.UserDisplayName: user172818
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-09T10:55:15.573Z
Comments.Text: I started off with foldseek but I need lower resolution search.
Comments.UserDisplayName: Johnny Tam
Tags: <protein-structure>
Title: Protein fold topology search web-server
ThreadText: # Protein fold topology search web-server
  
  (Asked by: username_0 on 2023-05-08)
  
  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](https://i.sstatic.net/UE70k.png)](https://i.sstatic.net/UE70k.png)
  
  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.
  
  ADD COMMENT • link • edit •
  
  **Tags:** protein-structure
  
  > **Comments:**
  > **username_1**: Have you tried [foldseek](https://search.foldseek.com/search)?  
  > **username_0**: I started off with foldseek but I need lower resolution search.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-05-09. Score: 1
  
  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.
  
  
  ---
  
  