Hi all,

I am conducting research on screening peptides (20-35 amino acids) with potential for treating dengue fever through protein-peptide docking methods. In the protein database, I found the target protein in both unbound (apo) and complex-bound (holo) forms. Which form of the target protein should I choose for docking? Additionally, the preparation steps for proteins and peptides before docking that I have learned include: adding missing amino acids, removing water, adding hydrogen, and recalculating charges. Are these all the necessary preparation steps before docking? The servers I have chosen to perform docking are: ClusPro, HADDOCK and HawkDock. Should I prepare the input files the same way for all of them? Please advise me or provide relevant references. I am new to this field and facing many difficulties. Please help me. Thank you.