Hi Luigi, All of the molecular docking programs are trying to predict the best pose, but nothing is perfect. These are research questions that you will need to decide for yourself, but also by applying anything you already know about your specific protein, and reading documentation about the docking programs, and research papers where other people did docking (to see what protocols were used). ChimeraX does not do molecular docking and we are not developers of these methods. So it would be better to look at the Autodock Vina website for information <https://vina.scripps.edu/> ...and ask questions in some other place like the AutoDock mailing list <https://vina.scripps.edu/questions/> <https://autodocksuite.scripps.edu/support/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 21, 2023, at 1:10 AM, Luigi Marongiu, PhD via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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