Post-docking refinement or not?

HADDOCK
1

I submitted 2 PDB structures via Haddock 2.4 web server.
I obtained several clusters and I considered the first one with HS (49) and z-score (-1,1) lower than the other clusters. Then I selected the first model structure (interaction complex) of the cluster and I submitted it via refinement tool (haddock 2.4 website). Then I selected the final model on the basis of FNAT, L-RMSD and I-RMSD values.
Is this method correct? Or can I consider only the first cluster that I obtained, without making any refinement?

Thank you.

2

The refinement will not change your model. So the selection is basically made at the first stage.

I would always look at the various clusters and not blindly trust numbers.
Ideally the models should explain some mutations, conservation, …

Note that you the cluster that you select has a positive score. Most likely your restraints are violated.

4

That one looks quite ok. But there are of course no restraints for refinement.

You should look at other clusters as well.

Check also our online tutorials, especially if this is your first encounter with docking!

https://www.bonvinlab.org/education/HADDOCK24

I would start with the basic protein-protein one.

5

thank you!!