# Docking drugs in membrane protein cavity
**URL:** https://ask.bioexcel.eu/t/docking-drugs-in-membrane-protein-cavity/3648
**Category:** HADDOCK
**Created:** [April 3, 2022, 5:13pm UTC](https://ask.bioexcel.eu/t/docking-drugs-in-membrane-protein-cavity/3648 "2022-04-03T17:13:43Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@f.pettini](https://ask.bioexcel.eu/u/f.pettini)
#### Post date: [April 3, 2022, 5:13pm UTC](https://ask.bioexcel.eu/t/docking-drugs-in-membrane-protein-cavity/3648/1 "2022-04-03T17:13:44Z")
Dear Prof Bonvin and All,
I am interested to dock some drugs in the cavity of a membrane protein; process and analysis proceed correctly, even if in some cases the drugs is docked outside the binding-site of the cavity (just under the selectivity filter). I suppose the issue is in the selection of active/passive residues, so I would gently to know if there is a way to select a box with center and size coordinates, such as in Autodock.
I can share all files if needed. Thanks in advance.
Francesco
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### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 5, 2022, 1:51pm UTC](https://ask.bioexcel.eu/t/docking-drugs-in-membrane-protein-cavity/3648/2 "2022-04-05T13:51:56Z")
Hi Francesco
> I am interested to dock some drugs in the cavity of a membrane protein; process and analysis proceed correctly, even if in some cases the drugs is docked outside the binding-site of the cavity (just under the selectivity filter). I suppose the issue is in the selection of active/passive residues, so I would gently to know if there is a way to select a box with center and size coordinates, such as in Autodock.
You can’t define a box like in autodock.
Two options:
1. Define active residues lining up the box
2. Define a shape into the binding site and define restraints to that shape. Check for that the following tutorial:
[https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/](https://www.bonvinlab.org/education/HADDOCK24/shape-small-molecule/)
Also, if your binding site is rather buried, decreasing the intermolecular interactions might help getting the ligand into it (step 10 in the above tutorial).
Cheers
Alexandre