CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		ProbKnot
MCC	0.746	>	0.414
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.414 ± 0.020
Sensitivity	0.681	>	0.403
Positive Predictive Value	0.818	>	0.425
Total TP	1989	>	1178
Total TN	7954946	>	7954602
Total FP	607	<	1805
Total FP CONTRA	71	<	260
Total FP INCONS	371	<	1337
Total FP COMP	165	<	208
Total FN	931	<	1742
P-value	0.0

Comparison of performance of PPfold(20) and ProbKnot. 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 ProbKnot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for PPfold(20) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and ProbKnot. 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 ProbKnot).

Total Scores
MCC	0.746
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127
Sensitivity	0.681
Positive Predictive Value	0.818
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.82	0.78	0.87	363	1192324	70	13	40	17	105
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.64	0.56	0.73	280	1627728	143	17	85	41	222
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.56	0.49	0.64	246	1674980	178	15	124	39	261
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.85	0.81	0.90	367	1119348	69	4	37	28	85
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.83	0.81	0.86	374	1135845	75	15	44	16	90
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.78	0.68	0.88	359	1204721	72	7	41	24	168

Total Scores
MCC	0.414
Average MCC ± 95% Confidence Intervals	0.414 ± 0.020
Sensitivity	0.403
Positive Predictive Value	0.425
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00256	SSU_rRNA_bacteria links to Rfam database...	0.40	0.40	0.41	185	1192284	296	39	232	25	283
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.40	0.41	0.40	207	1627588	371	65	250	56	295
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.40	0.40	0.39	202	1674852	365	59	252	54	305
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.41	0.39	0.43	176	1119350	259	29	201	29	276
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.46	197	1135851	249	39	191	19	267
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.43	0.40	0.47	211	1204677	265	29	211	25	316

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