CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Afold
MCC	0.801	>	0.764
Average MCC ± 95% Confidence Intervals	0.821 ± 0.143	>	0.812 ± 0.151
Sensitivity	0.774	<	0.781
Positive Predictive Value	0.837	>	0.755
Total TP	205	<	207
Total TN	13799	>	13770
Total FP	69	<	108
Total FP CONTRA	6	<	16
Total FP INCONS	34	<	51
Total FP COMP	29	<	41
Total FN	60	>	58
P-value	5.86050763602e-08

Comparison of performance of ContextFold and Afold. 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 ContextFold and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Afold. 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 ContextFold and Afold).

Total Scores
MCC	0.801
Average MCC ± 95% Confidence Intervals	0.821 ± 0.143
Sensitivity	0.774
Positive Predictive Value	0.837
Nr of predictions	18

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	0.92	0.86	1.00	6	124	3	0	0	3	1
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
2LKR_A	-	0.70	0.66	0.76	19	2415	12	0	6	6	10
2LQZ_A	-	1.00	1.00	1.00	8	124	1	0	0	1	0
2LWK_A	-	1.00	1.00	1.00	11	196	1	0	0	1	0
3J0L_1	-	0.75	0.69	0.82	9	473	5	0	2	3	4
3J0L_h	-	0.95	0.91	1.00	29	2111	2	0	0	2	3
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.812 ± 0.151
Sensitivity	0.781
Positive Predictive Value	0.755
Nr of predictions	18

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.85	0.82	0.90	9	197	2	0	1	1	2
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

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