Yes, it's one of the most common and efficient servers for analyzing interactions between two proteins. ClusPro employs a Fast Fourier Transform (FFT)-based algorithm for protein docking.

For a better understanding, this paper may help you out Article ClusPro: A fully automated algorithm for protein-protein docking

Marjanur Rahman Bhuiyan Thank you for the answer.

I get stuck in analysis part, like when we do protein ligand docking, in that case we can analyse and visualize the interactions using pymol or discovery tools but how are we gonna do this in case of protein protein dockiing?

Another question is that in the case of ligand and protein, ligand sits very efficiently in the active site of protein as the ligand structure is small, but in case of protein protein, both structures are very large and what i think is that in that case protein will not be able to sit in the active site so in that case should we just consider the interaction of protein with the active site of another protein?