CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Pknots		NanoFolder
MCC	0.808	>	0.304
Average MCC ± 95% Confidence Intervals	0.860 ± 0.179	>	0.353 ± 0.351
Sensitivity	0.759	>	0.343
Positive Predictive Value	0.863	>	0.281
Total TP	126	>	57
Total TN	18883	>	18826
Total FP	30	<	159
Total FP CONTRA	2	<	22
Total FP INCONS	18	<	124
Total FP COMP	10	<	13
Total FN	40	<	109
P-value	0.0

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

Total Scores
MCC	0.808
Average MCC ± 95% Confidence Intervals	0.860 ± 0.179
Sensitivity	0.759
Positive Predictive Value	0.863
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...	0.86	0.74	1.00	20	2465	2	0	0	2	7
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	4	0	2	2	2
RFA_00770	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1999	3	0	0	3	1
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	4	1	0	3	0
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0

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.