Setting positions where the ligand will bind to the receptor

HADDOCK
1

Good day!

I am trying to dock the TRAIL ligand onto a trimer of Death Receptor 4. However, when I run the job onto the webserver, the results that I get are far from the experimental findings and have a positive HADDOCK score. Is there some way to set some restrains that the ligand would bind to the receptor in a fixed orientation? I have active sites in both receptor and ligand obtained from experimental studies.

Thank you!

2

There is a lot of flexibility in defining restraints.

May-be in your case the shape-restrained protocol might work best. Check the following tutorial:

https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/