Protein-DNA docking and Protein-UV induced DNA docking

HADDOCK
,
1

I am docking a protein on DNA(57 nucleotide long)
I want to compare 2 complexes:

  1. Protein’s binding to a normal DNA
  2. Protein’s binding to UV- induced CPD diners DNA

I have induced Thymine dimers in DNA and have the PDB file for it but when I docked the protein with this UV induced DNA, the resulting complexes no longer had those dimers.
The software removed them on its own

What should I do? As the dimers should be present as I want to see how it affects the binding of the protein to mimic binding under UV stress condition and check it’s efficiency compared to normal DNA binding.

2

I have induced Thymine dimers in DNA and have the PDB file for it but when I docked the protein with this UV induced DNA, the resulting complexes no longer had those dimers.
The software removed them on its own

What should I do? As the dimers should be present as I want to see how it affects the binding of the protein to mimic binding under UV stress condition and check it’s efficiency compared to normal DNA binding.

The server unfortunately does not support those.