After obtained the docking results (Protein-DNA), I can see which docking structure is the best among all predicted structure.
(1)Do you think I could use Fnat and i-RMSD of the highest scored structure to support that our docking model is a high-quality one? my reference is this paper
Only if you know the reference structure of the complex you are predicting. Otherwise you can not calculate those metrics.
The HADDOCK results pages do show such stats, but in that case the reference structure used is the best model generated.
(2) Empirically, how low a HADDOCK score can be considered as good? In my case, my best scored protein-DNA docking structure received a score of -83.4 +/- 6.9. Is it good enough?
There is no absolute values to define what is good or bad. In principle the electrostatic energy can go to minus infinity
What is good will depend on the type of the complex and the specifics of the molecules.
And remember: our HADDOCK scores IS NOT a free energy of binding.
Thank you amjjbonvin!
after read some literature, it looked like HADDOCK 2.2 was supposed to generate protein–DNA complex model(s) with available experimental data, like NMR spectroscopy.
If I only have predicted protein and DNA 3D structure, it looked like HADDOCK may not be very helpful in my case.
Am I right?
You can try to run HADDOCK in ab-initio mode (e.g. center of mass restraints), but without any information I would not trust much the models.
Unless you know which DNA sequence is being recognised, which would allow you to define a few active residues.
Also I do suggest to switch to using the 2.4 version of the server.