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Table 2
Sets of folds confused by both VAST and SHEBA.
	Sets of confused folds, S	Number of domains in S	Sheba FPR_S(%)	Sheba TPR_S(%)	Sheba FPR_S/TPR_S(%)	Vast FPR_S(%)	Vast TPR_S(%)	Vast FPR_S/TPR_S(%)	Explanation for confusion

1	a.28, a.39	50	29	57	51	10	16	64	4 helix bundle up-and-down (a.28), and 4 helix array of 2 hairpins folds. Confusion is caused by match of helices oriented similarly. Folds confused mostly by SHEBA.
2	a.46, a.52	9	45	97	46	7	36	20	4 helix bundle left and right-handed super helix (a.46), and 4 helix right-handed super helix folds. Confusion is caused by match of helices oriented similarly. Folds confused mostly by SHEBA.
3	a.47, a.7	24	87	88	98	8	20	40	3 helix bundle (a.7) and 4 helix bundle (a.47) folds. Confusion due to match of very similar structure. Folds confused mostly by SHEBA.
4	b.68, b.69, b.66, b.67, b.70	45	92	98	94	40	83	48	Beta-propellers (repetitive 4-stranded blades) folds, of 4, 5, 6, 7 or 8 blades depending on the fold. Confusion is caused by match of several 4-stranded blades among domains of these folds.
5	b.1, b.2, b.3, b.7, b.12.	297	19	66	29	32	68	48	Beta sandwich folds of 7, 8, 9 stranded-sheet, with Greek-key topology. The motif causing the confusion among folds is a sandwich, which is rather well matched between domains of these folds.
6	b.24, b.71	24	69	97	72	27	93	29	Sandwich fold, with 10 strands in 2 sheets, and "folded meander topology" fold (b.24), and folded sheet with Greek-key topology. Confusion is due to match of parts of the sheets of the common core of these folds.
7	b.60, b.61	30	63	90	70	57	78	74	Closed barrel, with meander topology. Confusion caused by good match of between barrel motifs of the common core.
8	b.43, b.49, b.58, b.44	39	42	71	59	32	72	44	Folds of closed barrel with Greek-key topology. Confusion is due the match of substantial part of the barrel common core, among domains of these folds.
9	b.107, b.4	4	100	100	100	25	100	25	Sandwich fold (b.4), and closed barrel fold (b.107). Confusion is caused by the good match between a deformed barrel motif and a sandwich motif.
10	b.34, b.38	62	69	67	103	19	49	39	Barrel folds, with meander topology. Confusion is caused by the match between the barrel common cores.
11	b.38, b.56	12	52	100	52	65	93	70	Open barrel (b.38) and closed barrel (b.56) folds. Confusion is caused by the match of the barrel.
12	b.10, b.19, b.13, b.18, b.22, b.23	91	42	76	55	16	54	29	Folds with common core motif of beta sandwich; the 2 sheets are made of 8, 9 or 10 strands depending on the fold, and with jelly roll topology. The confusion among these folds is caused by the match of the strands of the beta sandwich common core.
13	c.1, c.6	185	62	75	83	78	87	90	TIM barrel (c.1) and variant of beta/alpha barrel, with closed parallel beta-sheet barrel (c.6) folds. Confusion is caused by the match of almost the whole TIM barrel.
14	c.8, c.98	14	50	75	68	30	54	56	3 layer beta/beta/alpha (c.8) and 3 layer alpha/beta/alpha (c.98) folds. Confusion is caused by the match between common beta/alpha layers.
15	c.84, c.95	19	65	91	71	55	92	60	3 layer alpha/beta/alpha of 4 strands (c.84), and of 5 strands (c.95) folds. Match of the 3 layer alpha/beta/alpha common core causes the confusion.
16	c.101, c.73, c.27	7	11	100	11	49	100	49	3 layer alpha/beta/alpha folds, with 5, 6 or 8 strands depending on the fold. Confusion is caused by the match of the 3 layer alpha/beta/alpha common core.
17	c.100, c.28, c.25, c.24, c.30, c.78, c.108, c.116, c.31, c.114, c.3, c.4, c.49, c.59, c.16, c.57, c.44, c.48, c.2, c.33, c.32, c.34, c.23, c.62, c.65, c.5	334	24	80	31	51	92	56	3 layer alpha/beta/alpha folds, with beta sheet of 4, 5, 6 or 7 strands depending of the fold. 3 layer beta/beta/alpha with central of 5 strands for c.3. Confusion among 3 layer alpha/beta/alpha folds is caused by the match of the 3 layer alpha/beta/alpha common core. Confusion between 3 layer alpha/beta/alpha and beta/beta/alpha is caused by the match of the 2 layer beta/alpha.
18	d.13, d.173	7	26	93	28	43	86	50	Fold containing the 3 layer alpha/beta/alpha common core (d.130 and unusual fold containing a common core of beta-alpha-beta-alpha-beta-alpha-beta (d.173). Confusion caused by the match of some strands and helices.
19	d.65, d.67	7	47	46	102	60	64	93	2 layer alpha/beta sandwich fold. Confusion caused by the match of 2 layer alpha/beta sandwich common core.
20	d.181, d.212	5	50	60	83	17	60	28	Folds containing beta-alpha-beta units. Confusion caused by match on the alpha/beta layers.
21	d.10, d.50	14	34	66	51	40	61	66	2 layer alpha/beta folds. Confusion caused by match on the 2 layer alpha/beta common cores.
22	d.140, d.68	12	34	68	51	40	52	77	Fold with 2 layer beta/alpha sandwich common core. Confusion is caused by match of the 2 layer beta/alpha sandwich.
23	d.151, d.160	7	75	100	75	58	100	58	Beta-sandwich; duplication of alpha+beta (d.151), 4 layers: alpha/beta/beta/alpha; mixed beta sheets (d.160) folds. Confusion due to match of the alpha beta sandwich.
24	d.95, d.206, d.64	12	18	96	18	34	79	43	2 layer alpha/beta sandwich folds. Confusion caused by the match of the 2 layer alpha/beta sandwich.
25	d.11, d.40	5	100	100	100	67	100	67	2 layer alpha/beta sandwich folds. Confusion caused by match of the 2 layer alpha/beta sandwich.
26	d.130, d.80, d.52	19	53	90	59	51	62	82	2 layer alpha/beta sandwich folds. Confusion is caused by the match of the 2 layer alpha/beta sandwich.
27	d.45, d.74, d.58, d.51, d.94, d.141, d.105	160	43	58	74	48	59	81	2 layer alpha/beta sandwich, and two beta-sheets and one alpha-helix packed around single core (d.141) folds. Confusion caused by match of the sheet and strands of the 2 layer alpha/beta sandwich core motif.
28	e.24, c.16, c.57, c.44, c.23, c.5	79	47	73	64	68	85	80	A domain component of a "multi-domain" domain of fold e.24 can matches the full domain of another fold which does not belong to the E class
29	e.4, c.48, c.2, c.32, c.33, c.34, c.23	178	35	74	48	74	87	85	A domain component of a "multi-domain" domain of fold e.4 matches the full domain of another fold which does not belong to the E class

Clusters of confused folds in VAST and SHEBA heat maps are reported. Rows 1 to 27 are intra-class clusters of confused folds found along the diagonal of the heat map. Only confusions in classes A, B, C and D are reported. Rows 28 and 29 are two off-diagonal clusters involving multi domains. Clusters and confused folds are listed in the order of appearance in the heat map. The heat maps of both methods obtained at 1% overall FPR were used to determined these clusters. Column 3 is the total number of domains within the set S. Columns 4 to 6 report the FPR_S, TPR_S(see Methods) and their ratios (in bold), for SHEBA, respectively, similarly, columns 7 to 9, report FPR_S, TPR_Sand their ratios (in bold), for VAST, respectively.
Sam et al. BMC Bioinformatics 2006 7:206 doi:10.1186/1471-2105-7-206

Table 2