Table 5.

Comparison with two existing methods

Ligands			AMP	ATP	FMN	GLC	NAD	ACR
Number of pocketsa			43/46	38/44	48/49	15/27	38/39	5/8
Rel.	P-S2.0		2.94	3.93	4.47	2.24	11.15	12.39
pAUC	eFSeekb		0.12	0.18	0.61	2.04	0.24	7.50
AUC	P-S2.0		0.74	0.78	0.80	0.61	0.88	0.88
	APocc		0.64	0.75	0.76	0.45	0.88	0.64
ADN	ANP	BCN	GLO	HEC	MLT	MPO	PLP	PMP
14/15	33	4/6	5/6	12/13	15/18	7	29/30	6/7
2.64	5.10	2.95	26.6	14.1	3.05	2.73	7.10	3.27
0.52	0.31	8.35	9.86	2.02	1.13	0.76	0.64	0.25
0.69	0.81	0.79	0.93	0.85	0.65	0.66	0.80	0.72
0.61	0.77	0.48	0.81	0.68	0.43	0.36	0.66	0.90

^aThe number of query pockets used for the comparison with eF-Seek (left) and Apoc (right). The numbers are different because common entries between the pocket databases by Patch-Surfer2.0 and eF-Seek were used as queries. Only one number is shown when the number were the same for eF-Seek and Apoc. The average AUC of receiver operator characteristic of the number of queries are shown.

^bFor the performance comparison with eF-Seek, we computed partial AUC (pAUC) that is the AUC computed up to the maximum false-positive rate (FPR) against the pAUC of the random retrieval up to the same FPR. Thus, rel_pAUC = pAUC/pAUC_random where pAUC = AUC/(1.0*maxFPR).

^cAPoc was run locally using the same database as Patch-Surfer2.0.