I have been trying to dock 2 peptides together, one of them phosphorylated at the serine. It seems that only the docking_local_refine option recognizes the phosphorylated group and generates an output. From what I understand, this option is used only when biological relevant information is available for the interaction interface. In the case where it is absent, is there other ways for the other docking options to work?
Greatly appreciate any help in this! =)