Hello,
I am trying to model the interactions of mutated SARS-CoV2 spike RBD with the ACE2 receptor, also looking at the wild type spike RBD. When trying to dock, should I be defining the active and passive residues for the mutated spike RBDs? I thought of using the ab-initio mode instead since I assume that the mutations in the RBD will lead to changes in the interacting residues. Or is this taken care of by the AIR mechanism of Haddock, where 50% of the residues are randomly chosen?
It won’t make sense to perform a full docking. Better to mutate the residues you want and only run the refinement in HADDOCK (we have a refinement interface in the server). Also check the following paper for an example of such a strategy for COVID:
Rodrigues, J. P. G. L. M., Barrera-Vilarmau, S., M C Teixeira, J., Sorokina, M., Seckel, E., Kastritis, P. L., & Levitt, M. (2020). Insights on cross-species transmission of SARS-CoV-2 from structural modeling. PLoS Computational Biology , 16 (12), e1008449. Insights on cross-species transmission of SARS-CoV-2 from structural modeling