CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		NanoFolder
MCC	0.380	>	0.230
Average MCC ± 95% Confidence Intervals	0.396 ± 0.185	>	0.307 ± 0.159
Sensitivity	0.339	>	0.249
Positive Predictive Value	0.432	>	0.221
Total TP	128	>	94
Total TN	67233	>	67104
Total FP	198	<	352
Total FP CONTRA	12	<	44
Total FP INCONS	156	<	287
Total FP COMP	30	>	21
Total FN	250	<	284
P-value	1.74172190343e-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	0.380
Average MCC ± 95% Confidence Intervals	0.396 ± 0.185
Sensitivity	0.339
Positive Predictive Value	0.432
Nr of predictions	11

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
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2M58_A	-	0.33	0.29	0.38	5	1640	8	1	7	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	7477	31	2	19	10	28
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3W3S_B	tRNA-Sec links to Rfam database...	0.50	0.45	0.56	18	4721	15	1	13	1	22
3ZEX_E	-	0.00	0.00	0.00	0	21892	55	2	51	2	77
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.61	0.86	30	6986	5	0	5	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4ATO_G	-	0.32	0.30	0.38	3	520	6	1	4	1	7
4JRC_A	-	0.24	0.22	0.29	5	1523	12	0	12	0	18

Total Scores
MCC	0.230
Average MCC ± 95% Confidence Intervals	0.307 ± 0.159
Sensitivity	0.249
Positive Predictive Value	0.221
Nr of predictions	11

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
2LKR_A	-	0.29	0.33	0.25	13	6054	38	8	30	0	26
2M58_A	-	0.43	0.47	0.40	8	1633	12	4	8	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3U4M_B	-	0.61	0.57	0.66	21	3128	11	1	10	0	16
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
3ZEX_E	-	0.03	0.04	0.03	3	21859	85	9	74	2	74
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4ATO_G	-	0.61	0.70	0.54	7	515	6	2	4	0	3
4JRC_A	-	0.48	0.48	0.50	11	1518	11	0	11	0	12

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