I am trying to dock two proteins together. I have carried out several jobs of the same proteins with the identical docking parameters. However, each job’s result gives me a different HADDOCK score, RMSD and Z-score.
Of course, the differences in scores are by +/- 5 but I would still like to know why there is a difference in scores if all the parameters and proteins are the same.
P.S. I am a student, and I am trying to compare binding affinities and energy of different protein complexes. I have learnt that a HADDOCK score is not indicative of binding affinity. I would highly appreciate if if I could receive some guidance on how to go about comparing binding affinities amongst different protein complexes. Thank you.