CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		MaxExpect
MCC	0.746	>	0.415
Average MCC ± 95% Confidence Intervals	0.747 ± 0.127	>	0.414 ± 0.016
Sensitivity	0.681	>	0.401
Positive Predictive Value	0.818	>	0.429
Total TP	1989	>	1170
Total TN	7954946	>	7954652
Total FP	607	<	1721
Total FP CONTRA	71	<	232
Total FP INCONS	371	<	1323
Total FP COMP	165	<	166
Total FN	931	<	1750
P-value	0.0

Comparison of performance of PPfold(20) and MaxExpect. 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 MaxExpect).
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 MaxExpect).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and MaxExpect. 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 MaxExpect).

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	0.415
Average MCC ± 95% Confidence Intervals	0.414 ± 0.016
Sensitivity	0.401
Positive Predictive Value	0.429
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	0.39	0.41	182	1192293	285	38	227	20	286
CRW_00326	SSU_rRNA_eukarya links to Rfam database...	0.41	0.41	0.42	205	1627618	330	55	232	43	297
CRW_00358	SSU_rRNA_eukarya links to Rfam database...	0.41	0.41	0.42	206	1674869	336	56	234	46	301
CRW_00590	SSU_rRNA_bacteria links to Rfam database...	0.40	0.37	0.43	169	1119363	246	23	201	22	283
CRW_00997	SSU_rRNA_bacteria links to Rfam database...	0.44	0.42	0.45	197	1135837	260	32	212	16	267
PDB_01120	SSU_rRNA_bacteria links to Rfam database...	0.43	0.40	0.46	211	1204672	264	28	217	19	316

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