Separate values are computed for the single-domain targets, the two-domain targets and all targets.

Ten CAFASP-DP methods have been evaluated:

1. Adda
2. Armadillo
3. Biozon
4. Dompred-domssea
5. Dompred-dps
6. Dopro
7. Mateo
8. SSep
9. Robetta-ginzu
10. Robetta-rosettadom

1. Absolute Number of Correctly Predicted Targets
In addition to the 10 domain prediction servers, three controls have been used: Control1, Control2 and Random. Control1 is computed by predicting all the targets as single-domain proteins and control2 is computed by predicting all the targets as two-domain proteins with a domain boundary at the centre of the sequence. The random control chooses between control1 and control2 at random. Finally, a consensus has been calculated based on a majority vote and some weighting scheme in case of a tie.

A prediction is considered as correct if the number of predicted domains is correct. For two-domain targets, the predicted domains should be continuous, i.e, with no split domains.

Methods	Number of targets predicted as single-domain	Number of targets predicted correctly as single-domain	Number of targets predicted as two-domain	Number of targets predicted correctly as two-domain	Number of targets predicted as multi-domain (number of domains >2) or split-domains
Control1	27	16	0	0	0
Control2	0	0	27	11	0
Random	14	8	13	5	0
ADDA	21	12	5	1	1
Armadillo	3	2	9	3	12
Biozon	2	2	12	4	13
Dompred-Domssea	23	15	4	3	0
Dompred-DPS	17	12	9	5	1
Dopro	18	13	8	5	1
Mateo	11	8	4	2	12
SSep	20	14	6	4	1
Robetta-Ginzu	10	9	13	6	4
Robetta-Rosettadom	13	11	11	6	3
CONSENSUS	18	13	7	5	2

2. Sensitivity and Specificity for single, two-domain and all targets

For each method, sensitivity (Sen) and specificity (Spec) have been calculated and plotted separately for single-domain targets, two-domain targets and finally for all targets as

Sen = TP / TP+FN

Spec = TP / TP+FP

where TP: Number of true positives; FN: Number of false negatives and FP: Number of false positives







3. Overlap Score (Single-Domain Targets)

Targets	Control1	Control2	Random	Adda	Armadillo	Biozon	Dompred-domssea	Dompred-dps	Dopro	Mateo	SSep	Robetta-ginzu	Robetta-rosettadom	Consensus
T0196	100.00	50.00	100.00	92.24	50.86	56.90	100.00	100.00	74.13	93.97	74.14	100.00	100.00	100.00
T0198	100.00	50.21	50.21	100.00	X	48.09	100.00	54.46	87.23	97.02	100.00	53.62	100.00	100.00
T0203	100.00	50.00	100.00	99.48	23.04	45.55	100.00	100.00	100.00	98.17	100.00	65.71	65.71	100.00
T0204	100.00	50.14	50.14	98.86	27.20	27.64	60.40	61.25	52.14	41.88	56.13	55.84	55.84	56.98
T0205	100.00	50.00	100.00	83.85	100.00	74.62	100.00	100.00	67.69	93.85	100.00	100.00	100.00	100.00
T0207	100.00	50.00	50.00	91.03	100.00	100.00	100.00	100.00	96.15	91.03	97.44	100.00	100.00	100.00
T0208	100.00	50.14	100.00	48.18	57.42	58.82	100.00	62.19	96.08	77.87	97.48	75.63	75.63	62.66
T0212	100.00	50.00	50.00	96.03	52.38	59.52	100.00	100.00	93.65	94.44	96.03	100.00	100.00	100.00
T0231	100.00	50.00	100.00	99.30	59.16	54.93	100.00	100.00	93.66	100.00	93.66	100.00	100.00	100.00
T0234	100.00	50.30	50.30	100.00	21.97	67.27	100.00	100.00	100.00	42.42	100.00	100.00	100.00	100.00
T0236	100.00	50.00	100.00	96.36	52.73	52.73	100.00	100.00	100.00	51.82	100.00	61.82	100.00	100.00
T0246	100.00	50.00	50.00	98.59	27.01	40.96	100.00	100.00	100.00	35.31	100.00	100.00	100.00	100.00
T0247	100.00	50.00	100.00	97.80	40.11	40.93	100.00	59.07	74.73	100.00	98.35	79.95	79.95	79.95
T0252	100.00	50.00	50.00	98.71	27.10	56.13	100.00	100.00	99.36	26.12	96.77	57.10	57.10	100.00
T0254	100.00	50.00	100.00	100.00	42.06	100.00	100.00	100.00	100.00	70.09	100.00	100.00	100.00	100.00
T0270	100.00	50.20	50.20	91.97	47.39	46.19	100.00	100.00	90.36	46.19	48.19	100.00	100.00	100.00
Average	100.00	50.09	75.05	88.85	42.26	50.15	97.53	87.73	85.97	59.89	91.14	79.22	86.44	92.22

*X: No prediction

4. Plot of overlap score vs the percentage of correctly predicted single-domain targets

5. Overlap Score (Two-Domain Targets)

Targets	Control1	Control2	Random	Adda	Armadillo	Biozon	Dompred-domssea	Dompred-dps	Dopro	Mateo	SSep	Robetta-ginzu	Robetta-rosettadom	Consensus
T0199	74.67	75.15	74.67	74.56	X	98.82	91.42	92.01	70.41	69.53	88.17	92.01	63.61	89.65
T0202	61.85	87.95	87.95	61.85	X	61.04	61.85	61.85	54.62	61.85	61.85	43.37	67.07	61.85
T0209	50.63	99.58	50.63	87.87	60.25	75.73	50.63	87.87	67.78	79.50	88.70	89.12	50.63	89.12
T0216	51.49	98.39	98.39	51.49	66.21	54.02	51.49	79.77	55.63	97.47	73.33	63.91	86.44	88.28
T0222	84.72	65.42	84.72	84.72	59.25	34.32	98.39	87.94	84.72	84.72	96.78	93.30	93.30	93.30
T0223	58.25	91.26	91.26	58.25	84.47	89.81	58.25	58.25	58.25	58.25	58.25	58.25	58.25	58.25
T0225	52.14	97.86	52.14	51.79	81.07	55.00	52.14	52.14	29.29	52.14	52.14	70.36	70.36	52.14
T0228	65.04	84.85	84.85	64.80	50.58	54.55	95.80	46.85	63.40	82.75	61.77	85.32	85.32	85.32
T0229	68.12	81.88	68.12	68.12	92.03	68.12	68.12	68.12	84.06	68.12	68.12	94.93	94.93	92.03
T0235	75.95	73.95	73.95	64.13	59.92	65.33	75.95	75.75	48.70	91.18	96.59	47.90	47.90	47.90
T0255	56.60	93.08	56.60	56.60	74.84	90.57	56.60	56.60	74.84	45.28	49.06	95.60	95.60	56.60
Average	63.59	86.31	74.84	65.83	57.15	67.94	69.15	69.74	62.88	71.89	72.25	75.82	73.94	74.04

*X: No prediction

6. Plot of overlap score vs the percentage of correctly predicted two-domain targets

7. Plot of average overlap score vs the percentage of correctly predicted total targets





8. Prediction Performance Separately on HM and FR targets

Number of HM targets: 16
Number of HM targets which are single-domain: 10
Number of HM targets which are two-domain: 6

Number of FR targets: 11
Number of FR targets which are single-domain: 6
Number of FR targets which are two-domain: 5