We would like to restrcuture the IL-2 for better binding with receptors - beta and gamma. We used tools to restructure IL2 and get a list of different variants. i.e. a list of PDB files. We hope to use computation method to find out the limited list of best structures before going to lab. So that we can focus on best group first to save time and resource.
It is supposed that the better variants can get stronger binding with the above two said receptors. At first, we tried Rosetta Docking protocol. We compared a known variant which has stronger binding than original IL-2. But the overall score and i_sc (interface score) of this variant is not as good the original IL-2.
Is that Rosetta Docking the right protocol for us to use in this case ? In addition to overall score and i_sc, any further scores there I need to look at for comparison?
Or should we use other protocols like InterfaceAnalyzer. If we use InterfaceAnalyzer, which output score that I need to pay attention for my own purpose ?