CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Fold		RDfolder
MCC	0.558	>	0.435
Average MCC ± 95% Confidence Intervals	0.479 ± 0.241	>	0.389 ± 0.217
Sensitivity	0.544	>	0.378
Positive Predictive Value	0.593	>	0.525
Total TP	105	>	73
Total TN	8120	<	8158
Total FP	76	>	67
Total FP CONTRA	19	>	13
Total FP INCONS	53	=	53
Total FP COMP	4	>	1
Total FN	88	<	120
P-value	0.0

Comparison of performance of Fold and RDfolder. 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 Fold and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for Fold and RDfolder. 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 Fold and RDfolder).

Total Scores
MCC	0.558
Average MCC ± 95% Confidence Intervals	0.479 ± 0.241
Sensitivity	0.544
Positive Predictive Value	0.593
Nr of predictions	9

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3ADB_C	-	0.86	0.85	0.88	28	1787	4	0	4	0	5
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

Total Scores
MCC	0.435
Average MCC ± 95% Confidence Intervals	0.389 ± 0.217
Sensitivity	0.378
Positive Predictive Value	0.525
Nr of predictions	9

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...	-0.03	0.00	0.00	0	514	14	3	11	0	18
3ADB_C	-	0.48	0.45	0.54	15	1791	13	1	12	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	11
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9

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