CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Pknots
MCC	0.715	>	0.644
Average MCC ± 95% Confidence Intervals	0.682 ± 0.240	<	0.698 ± 0.364
Sensitivity	0.644	<	0.659
Positive Predictive Value	0.802	>	0.640
Total TP	85	<	87
Total TN	9214	>	9184
Total FP	27	<	68
Total FP CONTRA	3	<	14
Total FP INCONS	18	<	35
Total FP COMP	6	<	19
Total FN	47	>	45
P-value	0.0

Comparison of performance of PPfold(20) and Pknots. 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 PPfold(20) and Pknots).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and Pknots. 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 PPfold(20) and Pknots).

Total Scores
MCC	0.715
Average MCC ± 95% Confidence Intervals	0.682 ± 0.240
Sensitivity	0.644
Positive Predictive Value	0.802
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7

Total Scores
MCC	0.644
Average MCC ± 95% Confidence Intervals	0.698 ± 0.364
Sensitivity	0.659
Positive Predictive Value	0.640
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12
4AOB_A	SAM links to Rfam database...	0.19	0.21	0.21	6	1409	23	3	19	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	2	0	0	2	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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