For docking studies we usually take nascent protein and after receptor preparation, we dock the energy minimized ligand. Meantime we also need to choose the docking site and what if we choose a grid, resulted in those interaction which accommodate those amino acid which are rarely free and moreover busy in protein protein interaction.
So in that condition how we evaluate our docking after when we know that these interactions that the docking pose is showing with those amino acids which are not free.
Vikash Kumar
Using different docking softwares and looking for similar pose will be helpful. Also you can run short MD ( Upto 10 ns) to see the stability of binding pose and thus interaction.
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