CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		NanoFolder
MCC	0.546	>	0.386
Average MCC ± 95% Confidence Intervals	0.701 ± 0.165	>	0.631 ± 0.182
Sensitivity	0.495	>	0.406
Positive Predictive Value	0.607	>	0.374
Total TP	201	>	165
Total TN	60064	>	59954
Total FP	153	<	289
Total FP CONTRA	10	<	38
Total FP INCONS	120	<	238
Total FP COMP	23	>	13
Total FN	205	<	241
P-value	2.41358941668e-08

Comparison of performance of Afold and NanoFolder. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for Afold and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Afold and NanoFolder. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for Afold and NanoFolder).

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.701 ± 0.165
Sensitivity	0.495
Positive Predictive Value	0.607
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	1	0	0	1	1
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	2	51	2	77
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ATO_G	-	0.32	0.30	0.38	3	520	6	1	4	1	7
4HXH_A	-	1.00	1.00	1.00	6	319	1	0	0	1	0

Total Scores
MCC	0.386
Average MCC ± 95% Confidence Intervals	0.631 ± 0.182
Sensitivity	0.406
Positive Predictive Value	0.374
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2LQZ_A	-	0.91	0.91	0.91	10	340	1	1	0	0	1
2LWK_A	-	0.83	0.77	0.91	10	485	2	0	1	1	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
3ZEX_E	-	0.03	0.04	0.03	3	21859	85	9	74	2	74
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4HXH_A	-	0.81	1.00	0.67	6	316	3	3	0	0	0

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.