Table 1.

Kendall’s For All Ligand Rankings, The Kendall’s τs for the initial Glide docking show slight fluctuations in different scoring schemes, but do not show any immense improvement

Docking function	Scoring method	Clustering methods
		XTAL	TICA	PCA	GROMOS	TICA CBA	PCA CBA	GROMOS CBA
XTAL Ens. AB	Minimum	0.23
	W. Avg.	–
	Avg.	0.27
Glide SP-AB	Minimum	0.20	0.18	0.18	0.22	0.12	0.28	0.12
	W. Avg.	–	0.21	0.20	0.18	0.17	0.24	0.21
	Avg.	–	0.20	0.21	0.25	0.20	0.24	0.23
Glide SP-AR	Minimum	0.13	0.14	0.13	0.13	0.11	0.11	0.09
	W. Avg.	–	0.08	0.07	0.10	0.09	0.05	0.07
	Avg.	–	0.12	0.07	0.09	0.07	0.06	0.09
Glide XP-AB	Minimum	0.20	0.11	0.11	0.12	0.11	0.24	0.14
	W. Avg.	–	0.10	0.08	0.08	0.11	0.17	0.15
	Avg.	–	0.11	0.08	0.07	0.12	0.19	0.17
Glide XP-AR	Minimum	0.13	0.14	0.10	0.12	0.11	0.09	0.13
	W. Avg.	–	0.10	0.07	0.04	0.07	0.03	0.11
	Avg.	–	0.11	0.07	0.06	0.04	0.04	0.08
Glide SP-HB	Minimum	0.09	0.17	0.14	0.18	0.23	0.23	0.18
	W. Avg.	–	0.20	− 0.01	0.17	0.24	0.14	0.20
	Avg.	–	0.22	− 0.01	0.21	0.23	0.18	0.21
Glide SP-HR	Minimum	0.12	0.18	0.13	0.11	0.16	0.17	0.15
	W. Avg.	–	0.13	0.09	0.08	0.15	0.11	0.13
	Avg.	–	0.15	0.11	0.12	0.14	0.13	0.14

Here we show the Kendall’s τ from rank orderings produced through various docking functions, clustering methods, and scoring schemes. Docking Functions are labeled accordingly: XTAL Ens Crystal Ensemble, SP Glide Standard Precision Docking, XP Glide Extra Precision Docking, A apo structure, H holo structure, B blind docking, R restrained docking. We experimented with these scoring schemes to test if a particular method of discerning scores for each ensemble would better represent the protein binding mechanisms and improve rank ordering. The various scoring schemes were the Minimum, Weighted Average (W. Avg.), and Average (Avg.)