2 Protein-1 DNA Docking

HADDOCK
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1

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

2

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