How to interpret HADDOCK Result?

Good day, I am an undergraduate and doing a protein-protein docking, I conducted to trial with my proteins, and I am having a hard time interpreting the result that I have obtained, is this a good or bad result? I’ve already tried to read the available literature, yet I can’t find information about what is a bad and good HADDOCK result. Thank you!

Trial 1:
HADDOCK score -42.7 +/- 23.5
Cluster size 3
RMSD from the overall lowest-energy structure 35.8 +/- 0.1
Van der Waals energy -47.5 +/- 10.9
Electrostatic energy -372.1 +/- 121.8
Desolvation energy 28.8 +/- 5.9
Restraints violation energy 503.9 +/- 104.5
Buried Surface Area 2320.1 +/- 573.3
Z-Score -1.9

Trial 2:
HADDOCK score -99.4 +/- 4.5
Cluster size 43
RMSD from the overall lowest-energy structure 8.8 +/- 0.5
Van der Waals energy -46.0 +/- 8.5
Electrostatic energy -447.4 +/- 96.0
Desolvation energy 30.3 +/- 8.3
Restraints violation energy 58.0 +/- 20.8
Buried Surface Area 2568.2 +/- 61.0
Z-Score -1.4

The score differences you observe come mainly from the restraint energy,

The HADDOCK score contains 10% of the restraint energy.

You must have given different information to drive the docking with the second trial satisfying better the restraints.

There is absolute scale of what is a good or bad score. It all depends on the system you are modelling and the restraints you are using.

Check our education page for various tutorials and also our best practice page:

[

HADDOCK Tutorials for version 2.4
bonvinlab.org

](HADDOCK Tutorials for version 2.4 – Bonvin Lab)

[

– Bonvin Lab
bonvinlab.org

](– Bonvin Lab)