Table 1.

Prediction performances with different preparations of chemical structures in the DeepSnap.

					AUC		Acc		MCC
Train:val:test	Protonation	Coordinate	Protonation	Coordinate	Average	SD	Average	SD	Average	SD
1:1:1	none	2D			0.930	0.006	0.967	0.007	0.821	0.035
1:1:1	dominate	2D			0.904	0.011	0.926	0.048	0.668	0.131
1:1:1	neutralize	2D			0.890	0.006	0.919	0.032	0.619	0.115
1:1:1	none	3D			0.907	0.008	0.797	0.035	0.440	0.019
1:1:1	dominate	3D			0.971	0.003	0.927	0.001	0.734	0.005
1:1:1	neutralize	3D			0.924	0.007	0.969	0.003	0.827	0.017
1:1:1	none	CORINA			0.989	0.003	0.958	0.003	0.826	0.012
1:1:1	dominate	CORINA			0.996	0.002	0.982	0.005	0.914	0.021
1:1:1	neutralize	CORINA			0.998	0.002	0.991	0.006	0.954	0.026
1:1:1	neutralize	3D	neutralize	CORINA	0.798	0.016	0.707	0.020	0.302	0.018
4:4:1	none	2D			0.923	0.024	0.959	0.029	0.798	0.107
4:4:1	dominate	2D			0.906	0.013	0.894	0.069	0.609	0.139
4:4:1	neutralize	2D			0.898	0.019	0.903	0.059	0.621	0.125
4:4:1	none	3D			0.911	0.009	0.801	0.043	0.458	0.033
4:4:1	dominate	3D			0.972	0.003	0.928	0.012	0.739	0.030
4:4:1	neutralize	3D			0.927	0.011	0.971	0.002	0.839	0.010
4:4:1	none	CORINA			0.990	0.003	0.957	0.009	0.821	0.029
4:4:1	dominate	CORINA			0.997	0.001	0.985	0.003	0.927	0.015
4:4:1	neutralize	CORINA			0.999	0.001	0.993	0.005	0.966	0.023
4:4:1	neutralize	3D	neutralize	CORINA	0.802	0.014	0.684	0.043	0.311	0.021

Parameters (angle: 280, MPS: 100, ZF:100, AT: 23%, BR: 14.5 mÅ, BMD: 0.4 Å, BT: 0.8 Å, LR: 0.0008, BS: 108, GoogleNet), n = 3 or 9 for 1:1:1 or 4:4:1, respectively. Maximum values for AUC, Accuray in test dataset (Acc), and Matthews correlation coefficient (MCC) in each dataset are indicated by bold.