# Generating Active Sites for Developed Protein

**URL:** <https://ask.bioexcel.eu/t/generating-active-sites-for-developed-protein/627>\
**Category:** HADDOCK\
**Created:** [November 20, 2017, 3:25pm UTC](https://ask.bioexcel.eu/t/generating-active-sites-for-developed-protein/627 "2017-11-20T15:25:50Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![adammccolgan](https://avatars.discourse-cdn.com/v4/letter/a/d07c76/32.png) [@adammccolgan](https://ask.bioexcel.eu/u/adammccolgan)\
**Post date:** [November 20, 2017, 3:25pm UTC](https://ask.bioexcel.eu/t/generating-active-sites-for-developed-protein/627/1 "2017-11-20T15:25:50Z")

</div>

Hi, I’m investigating the binding mechanisms for proteins in relation to peptides as part of my research. The protein (the larger protein) isn’t directly from a pdb file, it has been altered so that only the region of interest is present as opposed to the entire sequence. Does anybody know where I would go about locating the active residues for this?

---

<div class="post-metadata">

**Author:** ![mtrellet](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/mtrellet/32/42_2.png) [@mtrellet](https://ask.bioexcel.eu/u/mtrellet)\
**Post date:** [November 21, 2017, 9:20am UTC](https://ask.bioexcel.eu/t/generating-active-sites-for-developed-protein/627/2 "2017-11-21T09:20:47Z")

</div>

Hello,

I am not sure I totally understood your question, do you have a PDB file with the part of the protein you want to dock? And do you have a similar PDB files for the peptide? If you have both and do not have experimental data to drive the docking with HADDOCK, you can use BioInformatics prediction. We provide a web portal called CPORT that can be used to predict active and passive residues preliminary to a HADDOCK run: [https://milou.science.uu.nl/services/CPORT/](https://milou.science.uu.nl/services/CPORT/)

That’s a good start if you really have no data at hands to drive your docking run.

Cordially,

Mikael

---

<div class="post-metadata">

**Author:** ![adammccolgan](https://avatars.discourse-cdn.com/v4/letter/a/d07c76/32.png) [@adammccolgan](https://ask.bioexcel.eu/u/adammccolgan)\
**Post date:** [November 22, 2017, 8:32am UTC](https://ask.bioexcel.eu/t/generating-active-sites-for-developed-protein/627/3 "2017-11-22T08:32:16Z")

</div>

Thank you, that was what I needed