CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Contrafold		NanoFolder
MCC	0.645	>	0.304
Average MCC ± 95% Confidence Intervals	0.673 ± 0.163	>	0.353 ± 0.351
Sensitivity	0.584	>	0.343
Positive Predictive Value	0.719	>	0.281
Total TP	97	>	57
Total TN	18894	>	18826
Total FP	45	<	159
Total FP CONTRA	7	<	22
Total FP INCONS	31	<	124
Total FP COMP	7	<	13
Total FN	69	<	109
P-value	0.0

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

Total Scores
MCC	0.645
Average MCC ± 95% Confidence Intervals	0.673 ± 0.163
Sensitivity	0.584
Positive Predictive Value	0.719
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...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	1	0	0	1	6
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_01009	tRNA links to Rfam database...	0.46	0.52	0.41	11	2458	16	5	11	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	2004	5	0	2	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	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.