Side chains relevance in DiffDock predictions

[juangaropascual]

Analysing the docking performance of a protein predicted with different folding programs. I realised that the side chains configurations were playing a role in DiffDock prediction. It repeatedly appears in the paper that the exact position does not interfere.

"the fact that DIFFDOCK does not use the exact position of side chains in the score model and is therefore forced to implicitly model their flexibility"

To verify it, the side chains from a protein structure were predicted with three different methods using BetaSCPWeb. The backbone RMSD between the three structures is 0.000.

The plot of confidence versus rank shows that DiffDock prediction has clearly changed among side chains configurations. The same docking was run three times per each structure, always using the last version of DiffDock-L.

I would like to know if there is an explanation or if I am missing something.