<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>

CC BY-SA 4.0
2023-05-09T11:57:34.657Z
2023-05-09T11:57:34.657Z
gilleain
<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>

CC BY-SA 4.0
2023-05-09T00:18:26.653Z
Have you tried [foldseek](https://search.foldseek.com/search)?
user172818
CC BY-SA 4.0
2023-05-09T10:55:15.573Z
I started off with foldseek but I need lower resolution search.
Johnny Tam
<protein-structure>
Protein fold topology search web-server
# 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.  

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## 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.


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