# 2 Protein-1 DNA Docking

**URL:** <https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389>\
**Category:** HADDOCK\
**Tags:** haddock, support, community\
**Created:** [January 2, 2025, 7:33am UTC](https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389 "2025-01-02T07:33:10Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![pranav0903](https://avatars.discourse-cdn.com/v4/letter/p/a9a28c/32.png) [@pranav0903](https://ask.bioexcel.eu/u/pranav0903)\
**Post date:** [January 2, 2025, 7:33am UTC](https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389/1 "2025-01-02T07:33:10Z")

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I went through the basic Protein-DNA tutorial on HADDOCK2.4 website and followed all the steps.  
I applied symmetry restraints too.  
I did not apply any ambiguous or unambiguous restraints as I specified the active residues predicted through COACH server and also specified the passive residues.

Q1) I want to know if there are any other restraint or parameter I need to change as my molecule is the one which binds to DNA and wraps around it to protect it.

Q2) Which model should I choose from the results? The one with the highest haddock score or the one with the most negative Z score or the most positive Z score or a Z score closer to 0 as I read that it means the lowest deviation from the mean if it is closer to 2

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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:** [January 2, 2025, 10:34am UTC](https://ask.bioexcel.eu/t/2-protein-1-dna-docking/5389/2 "2025-01-02T10:34:19Z")

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> Q1) I want to know if there are any other restraint or parameter I need to change as my molecule is the one which binds to DNA and wraps around it to protect it.

Nothing special to change - you might have to refine your definition of restraint possibly depending on the results you get.

> Q2) Which model should I choose from the results? The one with the highest haddock score or the one with the most negative Z score or the most positive Z score or a Z score closer to 0 as I read that it means the lowest deviation from the mean if it is closer to 2

The cluster with the lowest (most negative) HADDOCK score.

But do check them all, especially if the scores overlap within standard deviations