Missing phosphate in protein-ssDNA docking

Hello, I´m having problems with docking results. I tryed to simulate protein-ssDNA docking (pdb files) but when analyze the Haddock results I can´t see all phosphates in ssDNA structure. Could somebody help me? What I have to do for solve this problem?
Appreciate any help.
Thank you.

What do you mean by “I can’t see all phosphate”?

Could we be indeed the termini ones are not there.
And don’t trust simply a graphical software, open the PDB files as a text file and check if they are present or not

Thank you for your quickly response. Sorry, I didn´t express myself clearly. The PO2 atoms of one of ssDNA termini aren´t there, neither in PDB file nor a text file. The HADDOCK replace a PO2 for one OH in one the termini. What I have to do to maintain the PO2 atoms in their place on ssDNA during docking? Would be that I need to change some parametres before run docking? I am new in doing this (Bioinformatics) so any help is very welcome.
Thank you.

That’s indeed the default behaviour of HADDOCK.

When using a local version you can however specify to keep the terminal phosphates by changing the linkage file.
This is something we could implement in the web server.

Ok. Thanks for your suggestion.
My best

Be patient - we should soon have the option in the 2.4 server :slight_smile:

@veross thanks for pointing this out to us! Whilist it is the default HADDOCK behaviour is to remove the terminal phosphates, having an option the option to keep them is a good idea!

Thus we have implemented it in the HADDOCK2.4 webserver. After uploading your DNA, select the option of Nucleic and you will see the new option. :man_technologist:t5:

Keep in mind that this is is not possible for protein-dna complexes inputed as a single molecule. :slight_smile:

Hi guys, first overall thank you for attention.
I tried a docking again after the update of HADDOCK but anyway it didn´t work for me. The phosphate in termini 5´of ssDNA is absent :frowning: When I analyze HADDOCK results the PO2 atoms aren´t there yet.

I am sending to you the receptor and ligand PDB files that I am using for that. The ssDNA (7c9c_DNA) was edited from PDB 7C9C chain D.
Maybe I am missing something important.

First I did a re-docking 7C9C chain A with ssDNA and the phosphate 5´ is absent. So I did a docking using my protein (dmc1single) and the phosphate 5´ is absent too. I would like to use the docking for run a molecular dinamic but when we tried to do this by GROMACS it seems impossible. We failed. Could you help me? If yes I really appreciate :slight_smile:

7c9c_ChainA.pdb (224.0 KB) 7c9c_DNA.pdb (42.1 KB) dmc1single_minimizado6.pdb (309.3 KB)

Can you share the link to your run?

Re-docking → https://wenmr.science.uu.nl/haddock2.4/run/7481920429/80346-teste6
Docking → https://wenmr.science.uu.nl/haddock2.4/run/7481920429/80347-teste7


We had to fix another unexpected issue. It is now working. Here is a run based on your submission:


Note that only the 5’ end phosphate is now kept. There is no phosphate on the 3’ end (i.e. one phosphate per base)

Hi, thank you for the test and for spend time with this but it still doesn’t work for me.
Yours ssDNA docked of “test-dna-P” link didn´t maintain PO2 in 5´ end instead added one PO3H in the 5´termini. So I did the docking and the re-docking one more time and PO2 aren´t there yet as you can see in the images below.
I only wish to maintain the PO2 in the 5´end like it is on the original file (7c9c_DNA) but I think it is impossible. We already tried to edit the input file before running docking in order to keep the phosphate but we didn´t get it because of the wrong protonations.
Like I said before this is not my area, I am still learning but for now
I can´t continuous. Anyway I appreciate your support and effort to solve the issues.
My regards

If I may give one suggestion (please take it carefully since I don’t know the full story of what you are analyzing): it seems that the termini are relevant for the interaction, one way of analyzing this would be to get some models from the top clusters given by haddock, manually add the termini and then run some molecular dynamics simulation on them, then analyze the fluctuations/distances/energies etc. It is out of the scope of HADDOCK but it might be useful to your project.

Good luck! :man_technologist:t4:

I am afraid we can’t do more than that.

For sure. We will try when it is possible.
Thank you guys.