Request for Guidance on Analyzing Protein-Protein Docking Results

Hi,

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

Cheers