I am currently using HADDOCK to study interactions between proteasome variants and an MHC peptide.
While running docking calculations, I tried an option that I believe was labeled something like “advanced” or “expert” settings (I am not entirely sure of the exact name). When I compared these results to those obtained with the default setup, I noticed substantial differences in the HADDOCK scores.
Although I am comparing the same systems (two proteasome variants with one peptide), the scores changed noticeably depending on the settings, which made me unsure how to interpret the results.
I wanted to ask whether this kind of variation is expected.
Do changes in advanced parameters significantly affect HADDOCK scores? Also, could you clarify what the main differences are between the default and these advanced settings?
I would like to make sure I am interpreting these results appropriately.
Thank you very much for your time and for developing HADDOCK.
Best regards,