<p>I'm not sure what you meant but you can take a look at <a href="http://genesilico.pl/NPDock" rel="nofollow noreferrer">NPDock</a> (disclaimer we wrote that tool). If you have a structure of your protein of interest, you can dock it to the structure of your DNA/RNA of interest. Mind that this is a rigid body docking which means that the structure will not change upon binding. </p>

CC BY-SA 3.0
2017-06-27T23:24:38.537Z
2017-06-28T09:05:20.913Z
2017-06-28T09:05:20.913Z
Marcin Magnus
<p>I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.</p>

<p>What tool can I use?</p>

CC BY-SA 3.0
2017-06-27T18:00:06.197Z
You mean a specific RNA molecule, right? Not any RNA in general?
terdon
CC BY-SA 3.0
2017-06-27T18:19:54.490Z
Autodock Vina is a common tool for ligand binding studies, if the stretch of RNA isn't too large I suspect it may work with Vina.
Joe Healey
<proteins><software-recommendation><rna><docking>
How can I dock a protein to a nucleic acid?
# How can I dock a protein to a nucleic acid?

(Asked by: username_0 on 2017-06-27)

I have a protein of interest and I would like to now how it interacts with RNA. I have structures of both molecules.

What tool can I use?

**Tags:** proteins, software-recommendation, rna, docking
> **Comments:**
> **username_1**: You mean a specific RNA molecule, right? Not any RNA in general?  
> **username_2**: Autodock Vina is a common tool for ligand binding studies, if the stretch of RNA isn't too large I suspect it may work with Vina.  

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## 1 answers

### Answer by username_3 on 2017-06-27. Score: 3 | Accepted answer

I'm not sure what you meant but you can take a look at [NPDock](http://genesilico.pl/NPDock) (disclaimer we wrote that tool). If you have a structure of your protein of interest, you can dock it to the structure of your DNA/RNA of interest. Mind that this is a rigid body docking which means that the structure will not change upon binding.


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