Hope you are in good health.
I am a biologist and would like to research on the interaction between two proteins using in silico approaches.
My project involves attachment of a ligand to protein and interaction this complex to another protein. In fact, this project has two phases.
First, I need to calculate the binding energy between Protein-Protein interaction (Phase I), next, make a complex of Protein-Ligand (using Auto Dock 4.2) and study on the attachment of this complex to another protein (Phase II).
Finally, I should compare the Phase I and II.
As far as I know, we cannot do a docking simulation of Protein-Ligand / Protein using most docking website servers.
Could you please tell me how to perform these docking? Or if there is any docking web server or software to perform this docking simulation? I mean (Ligand-Protein)/Protein interaction.
Thank you in advance,