I am having trouble describing my docking approach in haddock for a paper. As far as I understood from other discussions there is no difference between Molecule 1 and Molecule 2. However, I am writing in the paper “The molecule A was docked to the molecule B…” based on the fact that my molecule A was submitted under molecule 2 and molecule B was submitted under molecule 1. Since there is no difference between molecule 1 and 2 submission does that mean that I can write either “molecule A was docked to B” or “molecule B was docked to A” or maybe would it be completely wrong to write any of those phrases? Thanks!
Simply write: we docked molecule A and molecule B using HADDOCK…
The order in which you specify them in the server might impact the results (possible small numerical differences), but it remains the same system.