# How do I choose the active residues?

**URL:** <https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923>\
**Category:** HADDOCK\
**Tags:** haddock, support\
**Created:** [October 29, 2025, 12:49pm UTC](https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923 "2025-10-29T12:49:29Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![girish23](https://avatars.discourse-cdn.com/v4/letter/g/c0e974/32.png) [@girish23](https://ask.bioexcel.eu/u/girish23)\
**Post date:** [October 29, 2025, 12:49pm UTC](https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923/1 "2025-10-29T12:49:29Z")

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Hello, I have two proteins (X and Y); X has 2 chains (A and B), and Y has 1 chain. I want to dock Y with the B chain of X. I don’t understand how to choose the active residues, as the protein structure is not published yet. I predicted the structure, but I have no idea how to choose the active residues. I went through the manual too, but I am still not sure about it. Please help.

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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:** [October 30, 2025, 10:46am UTC](https://ask.bioexcel.eu/t/how-do-i-choose-the-active-residues/5923/2 "2025-10-30T10:46:09Z")

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Hi there

A few points:

- first you will have to treat your X molecule as a single chain without any residue overlap.

- if you don’t have any information about the binding sites (for both X and Y), best would be to try some ab-initio docking using center of mass restraints and increased sampling (10000 rigidbody models, and 400 for the subsequent steps). This does require guru access.

- you could eventually remove chain A, and at the end filter any model that would overlap with the A-B interface

And as alternative, did you try to run it through Alphafold (2 or 3)?