Comparing Docked Structures - one dsDNA with different proteins to assess/compare binding affinities

Hi All

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.

Docking scoring in any case poorly correlate with binding affinity…

In your case on molecule is a constant, which might make things better. Still it is a hard problem.