CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

Overview

Metric	ProbKnot		Afold
MCC	0.652	>	0.647
Average MCC ± 95% Confidence Intervals	0.722 ± 0.087	>	0.718 ± 0.084
Sensitivity	0.612	>	0.605
Positive Predictive Value	0.699	>	0.695
Total TP	797	>	788
Total TN	246221	<	246228
Total FP	392	<	398
Total FP CONTRA	62	>	58
Total FP INCONS	282	<	288
Total FP COMP	48	<	52
Total FN	505	<	514
P-value	0.000186465496926

^top

Performance plots

^top

Performance of ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

Total Base Pair Counts
Total TP	797
Total TN	246221
Total FP	392
Total FP CONTRA	62
Total FP INCONS	282
Total FP COMP	48
Total FN	505

Total Scores
MCC	0.652
Average MCC ± 95% Confidence Intervals	0.722 ± 0.087
Sensitivity	0.612
Positive Predictive Value	0.699
Nr of predictions	50

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.78	0.70	0.88	7	343	1	0	1	0	3
2KZL_A	-	0.83	0.74	0.93	14	1470	1	0	1	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	0	0	0	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.85	0.77	0.94	30	6073	4	0	2	2	9
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.88	0.85	0.92	11	484	1	0	1	0	2
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.26	0.24	0.29	10	5116	25	1	24	0	32
2YIE_X	-	0.34	0.33	0.36	4	1367	7	2	5	0	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	15	3	12	0	12
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3IYQ_A	tmRNA links to Rfam database...	0.28	0.31	0.26	29	60616	85	22	59	4	65
3IZ4_A	tmRNA links to Rfam database...	0.52	0.46	0.60	61	70774	46	6	35	5	71
3IZF_C	5S_rRNA links to Rfam database...	0.72	0.61	0.85	33	6864	6	0	6	0	21
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_1	-	0.76	0.63	0.92	12	1212	3	0	1	2	7
3J0L_h	-	0.77	0.65	0.90	28	6074	3	0	3	0	15
3NDB_M	-	0.77	0.69	0.88	42	9132	7	0	6	1	19
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	552	11	2	7	2	6
3NPB_A	SAM links to Rfam database...	0.72	0.61	0.85	28	6988	8	1	4	3	18
3O58_3	5_8S_rRNA links to Rfam database...	0.31	0.34	0.29	12	12362	41	4	25	12	23
3O58_2	5S_rRNA links to Rfam database...	0.76	0.76	0.76	29	7222	10	3	6	1	9
3OVS_D	-	0.92	0.92	0.92	12	548	1	0	1	0	1
3P22_G	-	0.96	0.92	1.00	11	730	1	0	0	1	1
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SIU_F	-	0.73	0.55	1.00	6	372	0	0	0	0	5
3SN2_B	IRE_II links to Rfam database...	1.00	1.00	1.00	12	394	0	0	0	0	0
3U4M_B	-	0.45	0.35	0.59	13	3138	9	1	8	0	24
3VJR_D	-	0.96	0.92	1.00	12	618	0	0	0	0	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.13	0.15	0.12	5	11738	49	7	31	11	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8

^top

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

Total Base Pair Counts
Total TP	788
Total TN	246228
Total FP	398
Total FP CONTRA	58
Total FP INCONS	288
Total FP COMP	52
Total FN	514

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.718 ± 0.084
Sensitivity	0.605
Positive Predictive Value	0.695
Nr of predictions	50

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2KXM_A	-	0.89	0.80	1.00	8	343	0	0	0	0	2
2KZL_A	-	0.86	0.74	1.00	14	1471	0	0	0	0	5
2L1F_B	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	24	2120	1	0	1	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.96	0.96	0.96	23	2056	1	0	1	0	1
2L2K_A	-	0.94	0.89	1.00	17	844	0	0	0	0	2
2L3C_B	-	0.91	0.82	1.00	14	547	0	0	0	0	3
2L3E_A	-	0.96	0.92	1.00	12	583	1	0	0	1	1
2L3J_B	mir-2985-2 links to Rfam database...	0.94	0.88	1.00	30	2455	0	0	0	0	4
2L5Z_A	-	0.86	0.75	1.00	9	316	0	0	0	0	3
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LBS_A	-	1.00	1.00	1.00	14	482	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	6	0	5	1	9
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LDT_A	-	0.85	0.73	1.00	11	454	0	0	0	0	4
2LHP_A	-	0.97	0.94	1.00	15	651	0	0	0	0	1
2LI4_A	-	0.93	0.88	1.00	14	482	0	0	0	0	2
2LJJ_A	-	1.00	1.00	1.00	8	343	2	0	0	2	0
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
2LQZ_A	-	0.85	0.82	0.90	9	341	1	1	0	0	2
2LWK_A	-	0.75	0.69	0.82	9	485	2	0	2	0	4
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.34	0.31	0.39	13	5118	20	1	19	0	29
2YIE_X	-	0.36	0.33	0.40	4	1368	8	2	4	2	8
2YIE_Z	-	-0.01	0.00	0.00	0	1525	16	3	12	1	12
3AKZ_H	tRNA links to Rfam database...	0.16	0.14	0.19	4	2680	17	2	15	0	24
3AM1_B	-	0.72	0.66	0.79	23	3211	6	0	6	0	12
3IYQ_A	tmRNA links to Rfam database...	0.31	0.34	0.29	32	60616	82	23	55	4	62
3IZ4_A	tmRNA links to Rfam database...	0.48	0.45	0.51	59	70760	58	11	46	1	73
3IZF_C	5S_rRNA links to Rfam database...	0.66	0.57	0.76	31	6862	10	1	9	0	23
3J0L_7	-	-0.01	0.00	0.00	0	1210	15	1	14	0	17
3J0L_1	-	0.73	0.63	0.86	12	1211	3	0	2	1	7
3J0L_h	-	0.73	0.60	0.90	26	6076	5	0	3	2	17
3NDB_M	-	0.84	0.74	0.96	45	9133	3	0	2	1	16
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3NMU_E	-	-0.01	0.00	0.00	0	553	10	1	7	2	6
3NPB_A	SAM links to Rfam database...	0.74	0.61	0.90	28	6990	5	0	3	2	18
3O58_3	5_8S_rRNA links to Rfam database...	0.34	0.34	0.34	12	12368	37	2	21	14	23
3O58_2	5S_rRNA links to Rfam database...	0.66	0.66	0.66	25	7222	14	4	9	1	13
3OVS_D	-	0.80	0.77	0.83	10	549	2	0	2	0	3
3P22_G	-	0.87	0.83	0.91	10	730	1	0	1	0	2
3R4F_A	-	0.96	0.92	1.00	23	2122	0	0	0	0	2
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SIU_F	-	0.85	0.73	1.00	8	370	0	0	0	0	3
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3VJR_D	-	0.96	0.92	1.00	12	618	1	0	0	1	1
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	43	5	26	12	28
4A4U_A	-	1.00	1.00	1.00	9	222	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.67	0.58	0.79	11	1261	3	1	2	0	8

^top

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 ProbKnot - scored higher in this pairwise comparison

1. Total counts & total scores for ProbKnot

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

Performance of Afold - scored lower in this pairwise comparison

1. Total counts & total scores for Afold

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