Hi everyone,

I'm conducting protein-protein docking using HADDOCK3 on 13,907 protein pairs in an ab initio mode due to lack of experimental information about my proteins. I have started to obtain results and now need to analyze my predictions, but I have some questions:

Do you have any examples of articles employing negative controls with proteins that are known not to interact? Is it mandatory to use a negative control?

I anticipate having numerous results with poor predictions to indicate that these pairs cannot interact and form a complex. I expected to have some positive scores and energies to suggest that the proteins do not interact, but currently, all my scores are negative. All the complexes exhibit negative scores and energies. I obtained some results with only one cluster and a few models within it, particularly when one of the proteins is disordered. Is it reasonable to conclude that if the prediction yields only one cluster, the interaction is likely not occurring?