# Docking of membrane proteins without TMD

**URL:** <https://ask.bioexcel.eu/t/docking-of-membrane-proteins-without-tmd/4886>\
**Category:** HADDOCK\
**Created:** [March 18, 2024, 11:22am UTC](https://ask.bioexcel.eu/t/docking-of-membrane-proteins-without-tmd/4886 "2024-03-18T11:22:19Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![karenf](https://avatars.discourse-cdn.com/v4/letter/k/b5ac83/32.png) [@karenf](https://ask.bioexcel.eu/u/karenf)\
**Post date:** [March 18, 2024, 11:22am UTC](https://ask.bioexcel.eu/t/docking-of-membrane-proteins-without-tmd/4886/1 "2024-03-18T11:22:19Z")

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I want to dock 2 membrane proteins that the structure is lacking the transmembrane domain (TMD), I only have the extracellular domains but I know which way the protein faces the membrane.  
How do I restrain the docking so it will be take into account this restriction?

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**Author:** ![karenf](https://avatars.discourse-cdn.com/v4/letter/k/b5ac83/32.png) [@karenf](https://ask.bioexcel.eu/u/karenf)\
**Post date:** [March 20, 2024, 10:23am UTC](https://ask.bioexcel.eu/t/docking-of-membrane-proteins-without-tmd/4886/2 "2024-03-20T10:23:20Z")

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I am using the web server

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [June 6, 2024, 1:02pm UTC](https://ask.bioexcel.eu/t/docking-of-membrane-proteins-without-tmd/4886/3 "2024-06-06T13:02:03Z")

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Dear Karen

There is no simple way of doing. One option would be to define a planar shape constituting of fake beads and define a few restraints from residues of your protein that you know to face the membrane to those beads. E.g.

```auto
assi (segid A and resi XX) (segid S) 0.0 0.0 0.0

```

where XX is the residue number of the amino acid facing the membrane. You should define for each of your proteins a few of those restraints.

The “shape” should be uploaded to the server as shape, with segid defined as S. Not that with a single layer, you might end up with proteins on both side depending on what is the information you have to drive the docking of your two proteins.

I am attaching here an example of such a shape (PDB file).

[planar-shape.pdb](https://ask.bioexcel.eu/uploads/short-url/sEw6kEMLcc9E0Qyj0NU2lnJh8yj.pdb) (9.7 KB)

Give it a try (if still needed).