CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	NanoFolder		MCFold
MCC	0.304	>	0.248
Average MCC ± 95% Confidence Intervals	0.353 ± 0.351	>	0.257 ± 0.179
Sensitivity	0.343	>	0.283
Positive Predictive Value	0.281	>	0.229
Total TP	57	>	47
Total TN	18826	>	18824
Total FP	159	<	173
Total FP CONTRA	22	>	16
Total FP INCONS	124	<	142
Total FP COMP	13	<	15
Total FN	109	<	119
P-value	0.0

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

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

Total Scores
MCC	0.248
Average MCC ± 95% Confidence Intervals	0.257 ± 0.179
Sensitivity	0.283
Positive Predictive Value	0.229
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	3287	34	3	31	0	25
PDB_00828	Purine links to Rfam database...	0.34	0.37	0.33	10	2455	22	1	19	2	17
PDB_00851	-	0.23	0.24	0.24	10	4711	32	0	32	0	31
PDB_01009	tRNA links to Rfam database...	0.43	0.52	0.35	11	2454	21	5	15	1	10
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1992	29	2	22	5	18
RFA_00773	Corona_pk3 links to Rfam database...	0.43	0.50	0.38	9	1929	16	4	11	1	9
RFA_00808	RydC links to Rfam database...	0.39	0.44	0.35	7	1996	19	1	12	6	9

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