# HADDCOK,Pretein-DNA

**URL:** <https://ask.bioexcel.eu/t/haddcok-pretein-dna/5316>\
**Category:** Uncategorized\
**Created:** [November 3, 2024, 6:38am UTC](https://ask.bioexcel.eu/t/haddcok-pretein-dna/5316 "2024-11-03T06:38:28Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![LvshuaiZhu](https://avatars.discourse-cdn.com/v4/letter/l/e0b2c6/32.png) [@LvshuaiZhu](https://ask.bioexcel.eu/u/LvshuaiZhu)\
**Post date:** [November 3, 2024, 6:38am UTC](https://ask.bioexcel.eu/t/haddcok-pretein-dna/5316/1 "2024-11-03T06:38:29Z")

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Hello! I have two questions regarding my task on protein-DNA binding. I am currently using HADDOCK to perform docking between proteins and DNA.

1. My protein is a novel protein, and I am unsure about the binding sites. Will randomly specifying a few residues affect the final result?
2. For the protein-DNA docking results, within what score range does it indicate a relatively strong binding affinity? Would a score below -100 be considered strong?

I look forward to your response. Thank you very much!