CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	McQFold		CentroidFold
MCC	0.594	>	0.482
Average MCC ± 95% Confidence Intervals	0.694 ± 0.092	>	0.548 ± 0.084
Sensitivity	0.583	>	0.430
Positive Predictive Value	0.611	>	0.548
Total TP	687	>	507
Total TN	158382	<	158581
Total FP	456	>	427
Total FP CONTRA	78	>	53
Total FP INCONS	359	<	365
Total FP COMP	19	>	9
Total FN	491	<	671
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of McQFold and CentroidFold. 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 McQFold and CentroidFold).
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 McQFold and CentroidFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for McQFold and CentroidFold. 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 McQFold and CentroidFold).

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Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

Total Base Pair Counts
Total TP	687
Total TN	158382
Total FP	456
Total FP CONTRA	78
Total FP INCONS	359
Total FP COMP	19
Total FN	491

Total Scores
MCC	0.594
Average MCC ± 95% Confidence Intervals	0.694 ± 0.092
Sensitivity	0.583
Positive Predictive Value	0.611
Nr of predictions	53

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2. Individual counts for McQFold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.19	0.20	0.21	4	1016	15	2	13	0	16
PDB_00020	-	0.75	0.65	0.87	13	765	2	0	2	0	7
PDB_00041	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00053	-	1.00	1.00	1.00	11	424	0	0	0	0	0
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	0.33	0.33	0.33	12	4150	24	0	24	0	24
PDB_00124	-	0.86	0.90	0.82	9	485	2	2	0	0	1
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.94	1.00	0.89	8	369	1	1	0	0	0
PDB_00209	-	0.96	1.00	0.92	11	549	1	1	0	0	0
PDB_00243	-	1.00	1.00	1.00	12	618	0	0	0	0	0
PDB_00352	-	0.86	0.79	0.94	15	1209	1	0	1	0	4
PDB_00370	-	0.00	0.00	0.00	0	15181	44	13	31	0	25
PDB_00447	-	0.11	0.11	0.12	5	7097	38	7	31	0	39
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	1	0	0	5
PDB_00713	-	0.43	0.43	0.45	9	1996	11	0	11	0	12
PDB_00716	HDV_ribozyme links to Rfam database...	0.68	0.70	0.67	16	2677	9	0	8	1	7
PDB_00804	-	0.00	0.00	0.00	0	15344	56	10	46	0	50
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.49	0.44	0.56	18	4721	14	0	14	0	23
PDB_00857	-	1.00	1.00	1.00	15	1066	0	0	0	0	0
PDB_00874	-	-0.02	0.00	0.00	0	928	18	0	18	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4147	39	0	39	0	40
PDB_00918	-	0.93	1.00	0.88	7	317	1	1	0	0	0
PDB_01009	tRNA links to Rfam database...	0.90	0.90	0.90	19	2464	5	0	2	3	2
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.88	1.00	0.78	7	222	2	2	0	0	0
PDB_01070	-	0.78	0.70	0.86	38	12676	6	0	6	0	16
PDB_01073	SAM links to Rfam database...	0.52	0.47	0.57	16	4343	13	2	10	1	18
PDB_01092	glmS links to Rfam database...	0.81	0.75	0.89	39	10109	6	1	4	1	13
PDB_01194	-	0.89	0.87	0.93	13	482	1	1	0	0	2
PDB_01201	-	0.88	0.77	1.00	17	1111	0	0	0	0	5
PDB_01203	-	0.74	0.68	0.81	13	1160	3	2	1	0	6
PDB_01250	-	0.17	0.15	0.19	6	12059	25	5	20	0	35
PDB_01260	-	0.92	0.92	0.92	23	1805	2	1	1	0	2
PDB_01281	-	-0.04	0.00	0.00	0	365	13	0	13	0	14
PDB_01299	-	0.71	0.67	0.77	10	890	3	1	2	0	5
PDB_01309	-	0.12	0.15	0.10	6	9122	56	12	40	4	33
RFA_00632	HDV_ribozyme links to Rfam database...	0.88	0.89	0.86	25	4066	4	3	1	0	3
RFA_00636	HDV_ribozyme links to Rfam database...	0.73	0.71	0.74	20	3978	7	5	2	0	8
RFA_00767	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
RFA_00769	Corona_pk3 links to Rfam database...	0.85	0.94	0.77	17	1931	5	4	1	0	1
RFA_00770	Corona_pk3 links to Rfam database...	0.88	0.78	1.00	14	2002	4	0	0	4	4
RFA_00773	Corona_pk3 links to Rfam database...	0.97	1.00	0.95	18	1934	5	1	0	4	0
RFA_00779	Corona_pk3 links to Rfam database...	0.97	0.94	1.00	17	1936	0	0	0	0	1
RFA_00808	RydC links to Rfam database...	1.00	1.00	1.00	16	2000	0	0	0	0	0
RFA_00809	RydC links to Rfam database...	0.79	0.81	0.76	13	2128	4	0	4	0	3

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Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

Total Base Pair Counts
Total TP	507
Total TN	158581
Total FP	427
Total FP CONTRA	53
Total FP INCONS	365
Total FP COMP	9
Total FN	671

Total Scores
MCC	0.482
Average MCC ± 95% Confidence Intervals	0.548 ± 0.084
Sensitivity	0.430
Positive Predictive Value	0.548
Nr of predictions	53

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2. Individual counts for CentroidFold [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00018	-	0.20	0.20	0.22	4	1017	14	2	12	0	16
PDB_00020	-	0.38	0.35	0.44	7	764	9	0	9	0	13
PDB_00041	-	0.70	0.50	1.00	6	624	0	0	0	0	6
PDB_00053	-	0.73	0.55	1.00	6	429	0	0	0	0	5
PDB_00056	-	0.93	0.88	1.00	14	616	0	0	0	0	2
PDB_00123	-	-0.01	0.00	0.00	0	4151	35	0	35	0	36
PDB_00124	-	-0.02	0.00	0.00	0	488	8	2	6	0	10
PDB_00128	-	0.80	0.71	0.91	10	485	1	0	1	0	4
PDB_00134	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00138	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00209	-	0.67	0.45	1.00	5	556	0	0	0	0	6
PDB_00243	-	0.63	0.58	0.70	7	620	3	0	3	0	5
PDB_00352	-	0.92	0.84	1.00	16	1209	0	0	0	0	3
PDB_00370	-	0.00	0.00	0.00	0	15219	6	0	6	0	25
PDB_00447	-	0.59	0.41	0.86	18	7119	3	3	0	0	26
PDB_00571	tRNA links to Rfam database...	0.77	0.64	0.94	16	3304	1	1	0	0	9
PDB_00713	-	0.54	0.48	0.63	10	2000	6	1	5	0	11
PDB_00716	HDV_ribozyme links to Rfam database...	0.33	0.30	0.37	7	2682	13	0	12	1	16
PDB_00804	-	0.22	0.24	0.21	12	15342	46	10	36	0	38
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00842	-	0.79	0.63	1.00	5	373	0	0	0	0	3
PDB_00851	-	0.44	0.39	0.50	16	4721	16	0	16	0	25
PDB_00857	-	0.77	0.60	1.00	9	1072	0	0	0	0	6
PDB_00874	-	-0.02	0.00	0.00	0	929	17	0	17	0	20
PDB_00886	-	-0.01	0.00	0.00	0	4148	38	0	38	0	40
PDB_00918	-	0.75	0.57	1.00	4	321	0	0	0	0	3
PDB_01009	tRNA links to Rfam database...	0.46	0.52	0.41	11	2458	16	5	11	0	10
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01040	-	0.30	0.30	0.32	6	1109	13	0	13	0	14
PDB_01059	-	0.75	0.57	1.00	4	227	0	0	0	0	3
PDB_01070	-	0.38	0.28	0.52	15	12691	14	0	14	0	39
PDB_01073	SAM links to Rfam database...	0.86	0.74	1.00	25	4346	1	0	0	1	9
PDB_01092	glmS links to Rfam database...	0.71	0.63	0.80	33	10112	10	1	7	2	19
PDB_01194	-	-0.02	0.00	0.00	0	487	9	0	9	0	15
PDB_01201	-	0.85	0.73	1.00	16	1112	0	0	0	0	6
PDB_01203	-	0.72	0.68	0.76	13	1159	4	3	1	0	6
PDB_01250	-	0.18	0.15	0.22	6	12063	21	5	16	0	35
PDB_01260	-	0.64	0.48	0.86	12	1816	2	0	2	0	13
PDB_01281	-	-0.03	0.00	0.00	0	366	12	0	12	0	14
PDB_01299	-	0.74	0.67	0.83	10	891	2	1	1	0	5
PDB_01309	-	-0.01	0.00	0.00	0	9118	62	9	53	0	39
RFA_00632	HDV_ribozyme links to Rfam database...	0.67	0.61	0.74	17	4072	6	1	5	0	11
RFA_00636	HDV_ribozyme links to Rfam database...	0.64	0.64	0.64	18	3977	10	4	6	0	10
RFA_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.45	0.44	0.47	8	1874	9	1	8	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1939	4	3	1	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.64	0.50	0.82	9	2005	4	0	2	2	9
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	3	1	0	2	8
RFA_00779	Corona_pk3 links to Rfam database...	0.68	0.56	0.83	10	1941	2	0	2	0	8
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.43	0.38	0.50	6	2133	6	0	6	0	10

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

Table of contents:

Overview

Performance plots

Performance of McQFold - scored higher in this pairwise comparison

1. Total counts & total scores for McQFold

2. Individual counts for McQFold [ download as .csv ]

Performance of CentroidFold - scored lower in this pairwise comparison

1. Total counts & total scores for CentroidFold

2. Individual counts for CentroidFold [ download as .csv ]