<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>

CC BY-SA 3.0
2017-05-17T03:45:52.300Z
2017-05-17T04:01:09.563Z
2017-05-17T04:01:09.563Z
Ashton Hellwig
<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>

<proteins><docking>
What are the optimal parameters for docking a large ligand using Hex?
# 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).


---

