I found a structure of a binary protein complex and tried to use it as my template to predict the combined structure of another 2 proteins. In this case, should I use the protein-protein docking protocol or the comparative modeling protocol? If I should use the protein-protein docking protocol, is there anyway for me to utilize the PDB file of the template structure to save me some work? And if I should use comparative modeling, how can I build a structure by inputting 2 queries? I assumed that homology modeling only deals with one input query?
Thanks a lot for any clarification.