<p>The quickest way to screen the PDB database is <em>Advanced Search</em> from either <a href="http://www.rcsb.org/" rel="nofollow noreferrer">RCSB</a> or <a href="https://www.ebi.ac.uk/pdbe/" rel="nofollow noreferrer">PDBe</a>.</p>

<p>Since you need entries with 2+ proteins you can set the number of protein chains to at least 2 in the RCSB search.  Or you can select "protein/protein complex" in <em>Assembly composition</em> in the PDBe search.</p>

<p>It's less clear how to search for inhibitors. If you'd look for the "inhibitor" word in the molecule names you'd get (together with the previous criterium) 1200+ entries.</p>

<p><a href="https://i.sstatic.net/O8mu5.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/O8mu5.png" alt="RCSB advanced search"></a></p>

CC BY-SA 4.0
2018-05-28T16:26:08.403Z
2018-05-28T16:26:08.403Z
marcin
<p>I looked up existing databases but ones like <a href="http://www.ippidb.cdithem.fr/" rel="nofollow noreferrer">iPPI-DB</a> or <a href="https://www.ebi.ac.uk/merops/inhibitors/" rel="nofollow noreferrer">enter link description here</a> either provide non-peptide inhibitors or only sequences. I need structures of proteins bound to other proteins, the latter of which is an inhibitor of the former, and the complex has a structure deposited in the PDB database. Here's an example: <a href="https://www.rcsb.org/structure/3U1J" rel="nofollow noreferrer">PDB:3U1J</a></p>

<p>In case there is no existing database in literature, it'd be great even if I can screen for such PDB entries using some code, but I can't come up with an algorithm for it. Thank you!</p>

CC BY-SA 4.0
2018-05-28T15:00:54.917Z
Welcome to the site @simple_dozer! I'm not sure if there is a code name to know if a protein is an inhibitor, but you can start by subsetting all the structures with at least two genes
llrs
<pdb>
How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?
# How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?

(Asked by: username_0 on 2018-05-28)

I looked up existing databases but ones like [iPPI-DB](http://www.ippidb.cdithem.fr/) or [enter link description here](https://www.ebi.ac.uk/merops/inhibitors/) either provide non-peptide inhibitors or only sequences. I need structures of proteins bound to other proteins, the latter of which is an inhibitor of the former, and the complex has a structure deposited in the PDB database. Here's an example: [PDB:3U1J](https://www.rcsb.org/structure/3U1J)

In case there is no existing database in literature, it'd be great even if I can screen for such PDB entries using some code, but I can't come up with an algorithm for it. Thank you!

**Tags:** pdb
> **Comments:**
> **username_1**: Welcome to the site @simple_dozer! I'm not sure if there is a code name to know if a protein is an inhibitor, but you can start by subsetting all the structures with at least two genes  

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## 1 answers

### Answer by username_2 on 2018-05-28. Score: 1

The quickest way to screen the PDB database is *Advanced Search* from either [RCSB](http://www.rcsb.org/) or [PDBe](https://www.ebi.ac.uk/pdbe/).

Since you need entries with 2+ proteins you can set the number of protein chains to at least 2 in the RCSB search. Or you can select "protein/protein complex" in *Assembly composition* in the PDBe search.

It's less clear how to search for inhibitors. If you'd look for the "inhibitor" word in the molecule names you'd get (together with the previous criterium) 1200+ entries.

[![RCSB advanced search](https://i.sstatic.net/O8mu5.png)](https://i.sstatic.net/O8mu5.png)


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