# Docking a peptide/protein in a receptor that trimerizes

**URL:** https://ask.bioexcel.eu/t/docking-a-peptide-protein-in-a-receptor-that-trimerizes/4468
**Category:** HADDOCK
**Created:** [August 28, 2023, 1:59pm UTC](https://ask.bioexcel.eu/t/docking-a-peptide-protein-in-a-receptor-that-trimerizes/4468 "2023-08-28T13:59:08Z")
**Posts on this page:** 1
**Page:** 1

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### Author: ![JIQuiambao](https://avatars.discourse-cdn.com/v4/letter/j/e19adc/32.png) [@JIQuiambao](https://ask.bioexcel.eu/u/JIQuiambao)
#### Post date: [August 28, 2023, 1:59pm UTC](https://ask.bioexcel.eu/t/docking-a-peptide-protein-in-a-receptor-that-trimerizes/4468/1 "2023-08-28T13:59:08Z")

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Good day!

I am attempting to dock a small peptide/protein onto human death receptors such as DR4 and DR5 in an attempt to see whether these small peptides/protein can bind to these receptors the same way death ligands do.

In literature, the biological ligands that bind to such receptors, death ligands, bind in a fashion that takes three such extracellular components of these receptors to form a trimeric complex. Three death receptors bind to a death ligand.

In docking, should I were to simulate the trimerization, would I consider three molecules of the same receptor plus the ligand, giving a total of 4 molecules in the Input Data tab of the webserver, and would I adjust the ‘Pair to active/passive selection set number(s)’ to just interact with the molecule number pertaining to the ligand that I want to dock? Say the receptors are Molecules 1, 2, and 3, while the ligand is 4. For Molecule 1, would I just set the ‘Pair to active/passive selection set number(s)’ to 4?

In addition, is it appropriate to enable Symmetry Constraints of C3 symmetry to the receptors that trimerize?

Thank you in advance!