Answers.Body: <p>While I have no experience with this <em>specific</em> question you have, according to Feinstein &amp; Brylinski (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468813/" rel="nofollow noreferrer">2015</a>), a "fully automated procedure", i.e. a Perl script, can be used to optimize the box size itself, and it can be found <a href="http://brylinski.cct.lsu.edu/content/docking-box-size" rel="nofollow noreferrer">here</a>.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-17T03:45:52.300Z
Answers.LastActivityDate: 2017-05-17T04:01:09.563Z
Answers.LastEditDate: 2017-05-17T04:01:09.563Z
Answers.UserDisplayName: Ashton Hellwig
Body: <p>I'm looking to dock a large ligand (~90kDa) to a receptor slightly larger receptor  (~125kDa) using Hex. If anyone is familiar with docking large structures, are there any recommended parameters for finding the best docking solution?</p>
  
  <p>Parameters in particular:</p>
  
  <ul>
  <li>Number of Solutions  </li>
  <li>N order of correlation for initial and final
  searches </li>
  <li>Receptor Range </li>
  <li>Ligand Range</li>
  </ul>
  
Tags: <proteins><docking>
Title: What are the optimal parameters for docking a large ligand using Hex?
ThreadText: # What are the optimal parameters for docking a large ligand using Hex?
  
  (Asked by: username_0 on 2017-05-16)
  
  I'm looking to dock a large ligand (~90kDa) to a receptor slightly larger receptor (~125kDa) using Hex. If anyone is familiar with docking large structures, are there any recommended parameters for finding the best docking solution?
  
  Parameters in particular:
  
  * Number of Solutions
  * N order of correlation for initial and final
    searches
  * Receptor Range
  * Ligand Range
  
  **Tags:** proteins, docking
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-05-17. Score: 1
  
  While I have no experience with this *specific* question you have, according to Feinstein & Brylinski ([2015](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468813/)), a "fully automated procedure", i.e. a Perl script, can be used to optimize the box size itself, and it can be found [here](http://brylinski.cct.lsu.edu/content/docking-box-size).
  
  
  ---
  
  