notesum.ai

Published at November 20

Unlocking the Power of Gradient Guidance for Structure-Based Molecule Optimization

q-bio.BM

cs.AI

Released Date: November 20, 2024

Authors: Keyue Qiu¹, Yuxuan Song¹, Jie Yu², Hongbo Ma³, Ziyao Cao¹, Zhilong Zhang⁴, Yushuai Wu¹, Mingyue Zheng², Hao Zhou¹, Wei-Ying Ma¹

Aff.: ¹Institute for AI Industry Research (AIR), Tsinghua University; ²Shanghai Institute of Materia Medica, Chinese Academy of Sciences; ³Department of Computer Science and Technology, Tsinghua University; ⁴Peking University

Arxiv: http://arxiv.org/abs/2411.13280v1

Methods		Vina Score ( $\downarrow$ )		Vina Min ( $\downarrow$ )		Vina Dock ( $\downarrow$ )		QED ( $\uparrow$ )	SA ( $\uparrow$ )	Div ( $\uparrow$ )	Success
Methods		Avg.	Med.	Avg.	Med.	Avg.	Med.	Avg.	Avg.	Avg.	Rate ( $\uparrow$ )
Reference		-6.36	-6.46	-6.71	-6.49	-7.45	-7.26	0.48	0.73	-	25.0%
Gen.	${\scriptsize{\showmycounter}⃝}$ AR	-5.75	-5.64	-6.18	-5.88	-6.75	-6.62	0.51	0.63	0.70	6.9%
	${\scriptsize{\showmycounter}⃝}$ GraphBP	-	-	-	-	-4.80	-4.70	0.43	0.49	0.79	0.1%
	${\scriptsize{\showmycounter}⃝}$ Pocket2Mol	-5.14	-4.70	-6.42	-5.82	-7.15	-6.79	0.57	0.76	0.69	24.4%
	${\scriptsize{\showmycounter}⃝}$ FLAG	45.85	36.52	9.71	-2.43	-4.84	-5.56	\ul0.61	0.63	0.70	1.8%
	${\scriptsize{\showmycounter}⃝}$ DiffSBDD	-1.44	-4.91	-4.52	-5.84	-7.14	-7.30	0.47	0.58	0.73	7.9%
	${\scriptsize{\showmycounter}⃝}$ TargetDiff	-5.47	-6.30	-6.64	-6.83	-7.80	-7.91	0.48	0.58	0.72	10.5%
	${\scriptsize{\showmycounter}⃝}$ DecompDiff	-5.19	-5.27	-6.03	-6.00	-7.03	-7.16	0.51	0.66	0.73	14.9%
	${\scriptsize{\showmycounter}⃝}$ IPDiff	-6.41	-7.01	-7.45	-7.48	-8.57	-8.51	0.52	0.59	\ul0.74	16.5%
	${\scriptsize{\showmycounter}⃝}$ MolCRAFT	-6.55	-6.95	-7.21	-7.14	-7.67	-7.82	0.50	0.67	0.70	26.8%
Oracle	${\scriptsize{\showmycounter}⃝}$ RGA	-	-	-	-	-8.01	-8.17	0.57	0.71	0.41	46.2%
Opt.	${\scriptsize{\showmycounter}⃝}$ DecompOpt	-5.75	-5.97	-6.58	-6.70	-7.63	-8.02	0.56	0.73	0.63	39.4%
Grad.	${\scriptsize{\showmycounter}⃝}$ TAGMol	-7.02	-7.77	-7.95	-8.07	-8.59	-8.69	0.55	0.56	0.69	11.1%
Opt.	${\scriptsize{\showmycounter}⃝}$ MolJO	\ul-7.52	\ul-8.02	\ul-8.33	\ul-8.34	\ul-9.05	\ul-9.13	0.56	\ul0.78	0.66	\ul51.3%
G + O	${\scriptsize{\showmycounter}⃝}$ MolJO^† (w=10)	-8.54	-8.81	-9.48	-9.09	-10.50	-10.14	0.67	0.79	0.61	70.3%