3D similarity pose-picking
Smina/Data-Warrior4.7.2
vinardo scoring function was used in the pose generation
First, the 154 test ligands were compared to the 20 published BACE ligands to find the most similar pair. Second, smina vinardo was excuted to dock the 154 test ligands.
Vinardo scoring function
add_box=2 #padding space of the ligand
Other parameters were set as default
Third, the most 3D similar pose (a python script was written to compute each pose's electron residue to determine the most 3D alike pose) was selected for affinity prediction.
No
Yes
NNScore
Yasara/Open Drug Discovery Toolkit
vina_gauss2, vina_repulsion, vina_hydrophobic, vina_hydrogen, vina_intra_gauss1, vina_intra_gauss2, vina_intra_repulsion, vina_intra_hydrophobic, vina_intra_hydrogen, vina_num_rotors
Post docking results were first minimized using Yasara. Next, oddt was used to predict pKi by using vina features for parameters, for NNScore
No
Yes