Dear all,

I am new to docking analysis. I have obtained a list of poses from VINA analysis, but what of them shall I choose?

Is the first the best choice?

The problem is that, according to the pose, the ligand binds the protein in a different position. Different ligands might or might not bind on the same position, thus choosing the right pose is essential to determine whether there is a position that allows binding of multiple molecules.

What is the procedure to determine whether such a multiple binding site exists?

What is the protocol to choose the right pose?

Thank you