CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		NanoFolder
MCC	0.594	>	0.304
Average MCC ± 95% Confidence Intervals	0.605 ± 0.118	>	0.353 ± 0.351
Sensitivity	0.560	>	0.343
Positive Predictive Value	0.637	>	0.281
Total TP	93	>	57
Total TN	18883	>	18826
Total FP	57	<	159
Total FP CONTRA	14	<	22
Total FP INCONS	39	<	124
Total FP COMP	4	<	13
Total FN	73	<	109
P-value	0.0

Comparison of performance of ProbKnot 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 ProbKnot and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot 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 ProbKnot and NanoFolder).

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.605 ± 0.118
Sensitivity	0.560
Positive Predictive Value	0.637
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	0.60	0.60	0.60	15	3296	10	6	4	0	10
PDB_00828	Purine links to Rfam database...	0.86	0.78	0.95	21	2463	1	0	1	0	6
PDB_00851	-	0.45	0.39	0.53	16	4723	14	0	14	0	25
PDB_01009	tRNA links to Rfam database...	0.54	0.57	0.52	12	2462	12	5	6	1	9
RFA_00770	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	2000	9	0	6	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	0	3	0	7

Total Scores
MCC	0.304
Average MCC ± 95% Confidence Intervals	0.353 ± 0.351
Sensitivity	0.343
Positive Predictive Value	0.281
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00571	tRNA links to Rfam database...	-0.01	0.00	0.00	0	3286	36	6	29	1	25
PDB_00828	Purine links to Rfam database...	0.30	0.33	0.28	9	2453	23	0	23	0	18
PDB_00851	-	0.16	0.17	0.17	7	4711	35	3	32	0	34
PDB_01009	tRNA links to Rfam database...	0.27	0.33	0.23	7	2455	25	3	20	2	14
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1996	24	0	20	4	18
RFA_00773	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1932	9	3	0	6	0
RFA_00808	RydC links to Rfam database...	0.83	1.00	0.70	16	1993	7	7	0	0	0

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