I have done protein docking with some relevant ligands, now i am looking for the best molecules on the basis of highest docked energy and the interest of amino acid interactions? is this the right way to find the good molecule on the basis of docking or what more i can do in the result analysis? which one is more reliable compound for protein having highest docked energy or lowest ?
*well i dont have any biological data for molecule to support as i am doing in a very new target.
moreover i have generated 10 poses for each molecule but every pose shows different interactions and different scores, so for choosing one specific molecule out of 100s i am pretty confused.
we have some specific interest of amino acids and depending on that i am planning to suggest some molecule however those molecules different poses interacts differently..so will that molecule work for the target..what are the chances..is there something we can do with the poses?