There exists numerous commercial and academic software packages which have used ligand similarity to predict ligand binding modes. Fukunishi et al. ranked docked poses based on the degree of overlap with reference ligand(s) . HYBRID and POSIT from OpenEye Scientific Software utilize a ligand-based scoring function which favorably scores similar shape and 3D alignment between query ligands and reference crystallographic ligands. Similar to HY-BRID and POSIT, SDOCKER has a modified CHARMMbased scoring function with an added similarity penalty. Alternatively, instead of modifying the scoring function in the above methods, PoPSS-Lite, developed by Kumar et al. places query ligands in the binding pocket in the closest possible conformation and orientation as the reference ligand and performs grid-based energy minimization to remove bad contacts.