Request for Guidance on Analyzing Protein-Protein Docking Results

Dear HADDOCK Team,

I hope this message finds you well.

I have performed docking simulations between proteins A and B, as well as between proteins A and C using the HADDOCK tool. From these simulations, I have obtained the following scoring metrics:

Cluster size
RMSD from the overall lowest-energy structure
Van der Waals energy
Electrostatic energy
Desolvation energy
Restraints violation energy
Buried Surface Area
However, I am uncertain about how to comprehensively analyze these metrics to determine whether the docking between A and B is better or worse compared to the docking between A and C. Therefore, I am seeking your expertise on how to scientifically and effectively compare these docking results based on the provided scoring metrics.

Thank you very much for your assistance.

Best regards,


The HADDOCK score should not be used to compare different complexes, but rather to inspect the results obtained within each run. Similar systems might be compared, but I don’t know how similar proteins B and C are in your case.

Have a look at this other thread Problem with interpretation HADDOCK scores

PS: I notice you have a very high restraint energy, maybe check your restraints and/or remove the 10% of that value from the overall HADDOCK score


Thank you :coffee:

I have connected A-B(TLR2) and A-C(TLR4). However, I can only perform kinetic simulations on one of these complexes, and I am struggling to find a reason to choose between them. Do you have any suggestions?

Thank you.

May-be some MD simulations first could help. Check for example:

Not really meant to compare different complexes though but rather different clusters of the same complex.