Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-27T23:24:38.537Z
Answers.LastActivityDate: 2017-06-28T09:05:20.913Z
Answers.LastEditDate: 2017-06-28T09:05:20.913Z
Answers.UserDisplayName: Marcin Magnus
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-27T18:00:06.197Z
Comments.Text: You mean a specific RNA molecule, right? Not any RNA in general?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-27T18:19:54.490Z
Comments.Text: 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.
Comments.UserDisplayName: Joe Healey
Tags: <proteins><software-recommendation><rna><docking>
Title: How can I dock a protein to a nucleic acid?
ThreadText: # 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.  
  
  ---
  
  ## 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.
  
  
  ---
  
  