Hello,
I have been docking different isoforms of a phosphodimer to a segment of DNA, and I have been noticing that almost all of resultant docks yield significantly distorted DNA.
Would there be any way to solve this issue through changing specific docking restraints or would this be caused due to the protein structure?
Thanks,
Are you using the server or a local version?
You should turn on (if not done by default - should be on the server), the DNA restraints.
I was using the server and I believe the restraints were selected, but I ended up getting docks with the strands of DNA separated and other distortions.
Some of the models were generated in March/April, would it be possible that the DNA restraints have not been auto-selected at that time?
I would suggest to repeat that docking and if the issue persist do share the ID so that we can take a look at your settings
I retried it and the models were much better, but the structure still was slightly distorted when I tried to run them through a protein-binding affinity predictor, is it possible that I missed another restraint or could it be an issue with the model (using two monomers instead of a homodimer)?
What do you mean by two different monomers? Each strand of the dna defined as separate chain?
If that’s the case then no restraints between the strands are automatically define.
Better to define it as a single chain for haddock
Sorry, I was refering to the two protein monomers, I previously used the double strand DNA and docked it to two identical monomers, but would dimerizing the monomers first and then using HADDOCK to dock the DNA to the dimer make a difference?