The influence of the experts' prior knowledge on the search results^a.

PDB	Ligand score (kcal mol−1)		Number of molecules (↑)		Average score (kcal mol−1, ↓)		QED (↑)		SA (↑)
	Test set	Baseline (Pocket2Mol)	Off	On	Off	On	Off	On	Off	On
1fmc	−9.32	−6.92	88	160	−9.52	−9.94	0.69	0.63	0.80	0.74
3g51	−7.63	−8.31	135	167	−9.55	−9.90	0.65	0.63	0.79	0.76
5q0k	−9.24	−6.67	15	58	−9.52	−9.90	0.63	0.66	0.80	0.80
1phk	−8.14	−10.72	433	737	−9.52	−10.09	0.65	0.66	0.76	0.75
4f1m	−6.58	−6.78	18	46	−9.29	−9.78	0.70	0.58	0.79	0.79
1e8h	−8.83	−8.72	264	353	−9.55	−10.08	0.70	0.65	0.78	0.77
1ai4	−6.28	−5.60	114	81	−9.41	−9.86	0.61	0.63	0.82	0.81
3w83	−3.91	−3.30	51	83	−9.54	−9.86	0.64	0.60	0.78	0.74
5d7n	−7.56	−7.71	128	114	−9.43	−9.97	0.63	0.65	0.78	0.77
5aeh	−11.93	−10.11	593	843	−10.26	−10.78	0.64	0.68	0.73	0.79
4qlk	−8.48	−7.34	238	366	−9.48	−9.97	0.57	0.66	0.76	0.80
3hy9	−8.12	−6.66	528	768	−9.51	−10.06	0.64	0.65	0.79	0.80
4m7t	−7.81	−8.24	525	701	−9.69	−10.07	0.65	0.64	0.76	0.78
Average	−7.99	−7.47	241	344	−9.56	−10.02	0.65	0.64	0.78	0.78

^a Off represents the standard 3D-MCTS, which only considers binding affinity as the reward; On represents a version of 3D-MCTS that incorporates domain knowledge based on pharmacophores during the generation process.