I have docked one dsDNA with 5 different proteins using HADDOCK Easy Interface(5 independent runs). I wish to know which protein has the strongest binding affinity to the dsDNA.
Please let me know how can I do that (because I read that docking/HADDOCK scores are not comparable). Moreover, in the HADDOCK result, the cluster having the best HADDOCK score also has 4 ‘Best Structures’. Which one to choose among them.
Please help. Thanks in advance.