I wonder if I have 3 docking runs using the same active residues involved in an protein-protein interaction:
How much it must be the difference in Pseudo Energy Score between the best cluster of each docking run to be significant to say that one is better than the other?
For instance, one run yielded a score of -74 and the other -112. Can I say that the last is better than the first one? By the way, this difference let me explain part of my experimental
Thank you in advance.
You have to also take into account the standard deviation of the score - the server reports the score as average of the best 4 models of each cluster together with the associated standard deviation.
In your case the score seem rather different to justify -112 as significantly better, but again check the standard deviations. If the restraints are the same, what causes then this difference? You are docking the same system (meaning same proteins)? If not, then it become difficult to compare scores…
Thank you Alexander for your fast answer!
I will take your piece of advice to re-analyse my results!!