0.2 | 0.3

Changes in PDB files used for clustering

Release 0.2 has 175 PDB files, release 0.3 has 199 PDB files, 161 of them are identical.

11 equivalence classes changed representatives: 1O0C → 1QRS, 2ZUE → 2ZUF, 2GIS → 3GX5, 3GCA → 3Q50, 3A3A → 3RG5, 2IPY → 3SNP, 3O30 → 3U5F, 3O58 → 3U5H, 3MUR → 3UCZ, 3PYO → 3V2F, 2NQP → 4AQ7.

27 new structures in release 0.3: 2Y8W, 2Y8Y, 2Y9B, 2Y9H, 3AMU, 3NVI, 3Q3Z, 3QSY, 3R9X, 3RKF, 3RW6, 3SD3, 3SIU, 3SLQ, 3SN2, 3SUX, 3T4B, 3TS0, 3TS2, 3TUP, 3U4M, 3V7E, 4A1B, 4A1C, 4AL5, 4AOB, 4ENB.

Obsolete: 2IPY → 3SNP, 3O30 → 4V7R, 3O58 → 4V7R, 3PYO → 4V83.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

Loading the Sankey diagram...

Changes in motif groups

Release 0.2 has 256 motif groups, release 0.3 has 245 motif groups, 47 of them are identical.

10 motif groups were updated, 199 groups are present only in release 0.2, 188 groups are only in release 0.3.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.

Identical motif groups

#	Motif id	Instances	Description
1	HL_58083.2	3
2	HL_19399.1	2
3	HL_65924.1	2
4	HL_98577.1	2
5	HL_57904.1	2
6	HL_88640.1	2
7	HL_38130.2	2
8	HL_05510.1	2
9	HL_17468.1	1
10	HL_26579.1	1
11	HL_48480.1	1
12	HL_65802.1	1
13	HL_83053.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
14	HL_94145.1	1	SSU Helix 43 (h43) Hairpin Loop E.coli
15	HL_30731.1	1
16	HL_53789.1	1
17	HL_84289.1	1
18	HL_97499.1	1
19	HL_20252.1	1
20	HL_33524.1	1	tRNA T-loop distorted by RS binding
21	HL_57217.1	1	cHS platform Intercalation Site
22	HL_66880.1	1
23	HL_84888.1	1	T-loop like but without tWH UA
24	HL_20806.1	1
25	HL_33640.1	1
26	HL_76027.1	1
27	HL_00238.1	1
28	HL_20914.1	1
29	HL_77981.1	1
30	HL_88921.1	1
31	HL_24707.1	1
32	HL_38138.1	1
33	HL_59610.1	1
34	HL_78507.1	1
35	HL_90365.1	1	5S rRNA Loop C from D.radiodurans
36	HL_10842.1	1
37	HL_25195.1	1
38	HL_38898.1	1
39	HL_61061.1	1
40	HL_79390.1	1
41	HL_91613.1	1
42	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
43	HL_25197.1	1
44	HL_45358.1	1	Double hairpin loop based on GGA triple
45	HL_63690.1	1
46	HL_79902.1	1
47	HL_93206.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_45018.2	4
2	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
3	HL_42687.2	3
4	HL_46794.2	3
5	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
6	HL_80492.2	3	tRNA D-loop
7	HL_19221.2	3
8	HL_27429.2	3
9	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
10	HL_24473.3	2	tRNA D-loop

Removed motif groups

#	Motif id	Instances
1	HL_69082.1	184
2	HL_05993.1	72
3	HL_72657.1	29
4	HL_47025.1	25
5	HL_91122.1	24
6	HL_94618.2	17
7	HL_81943.1	15
8	HL_32207.1	15
9	HL_78735.2	12
10	HL_18082.1	10
11	HL_80583.1	10
12	HL_26075.2	10
13	HL_83914.2	10
14	HL_54401.1	8
15	HL_58751.2	8
16	HL_95727.2	8
17	HL_06440.1	8
18	HL_07320.2	7
19	HL_95074.2	7
20	HL_70246.1	6
21	HL_40792.1	6
22	HL_68221.1	6
23	HL_41237.2	6
24	HL_49433.1	6
25	HL_88639.1	6
26	HL_03429.2	5
27	HL_03576.1	5
28	HL_31251.1	5
29	HL_06247.1	5
30	HL_31541.1	5
31	HL_60345.1	5
32	HL_82371.1	5
33	HL_91907.1	5
34	HL_20764.1	5
35	HL_29369.2	5
36	HL_96039.1	5
37	HL_29382.1	5
38	HL_01672.1	5
39	HL_85352.1	5
40	HL_02975.2	5
41	HL_54261.1	5
42	HL_69451.1	5
43	HL_07042.1	5
44	HL_32280.1	5
45	HL_77942.1	5
46	HL_38227.2	4
47	HL_84031.1	4
48	HL_06261.1	4
49	HL_11061.2	4
50	HL_06375.1	4
51	HL_20766.1	4
52	HL_41117.1	4
53	HL_52999.1	4
54	HL_22654.1	4
55	HL_32133.1	4
56	HL_36725.1	4
57	HL_57387.1	4
58	HL_62578.1	4
59	HL_44662.1	4
60	HL_83765.2	4
61	HL_05272.1	4
62	HL_20010.1	3
63	HL_42580.1	3
64	HL_65994.1	3
65	HL_00293.1	3
66	HL_17243.1	3
67	HL_47364.1	3
68	HL_54834.1	3
69	HL_66795.1	3
70	HL_04325.1	3
71	HL_52890.2	3
72	HL_85049.2	3
73	HL_18213.1	3
74	HL_62044.1	3
75	HL_77652.1	3
76	HL_44444.1	3
77	HL_69367.1	3
78	HL_93985.1	3
79	HL_18399.1	3
80	HL_49169.1	3
81	HL_18943.1	3
82	HL_75196.1	3
83	HL_75914.1	2
84	HL_89161.1	2
85	HL_08706.1	2
86	HL_12679.1	2
87	HL_70609.1	2
88	HL_76807.1	2
89	HL_12880.1	2
90	HL_42884.1	2
91	HL_55171.1	2
92	HL_77305.1	2
93	HL_84487.1	2
94	HL_00692.1	2
95	HL_13651.1	2
96	HL_31697.1	2
97	HL_48274.1	2
98	HL_77557.1	2
99	HL_80301.1	2
100	HL_83043.1	2
101	HL_92124.1	2
102	HL_13798.1	2
103	HL_32112.1	2
104	HL_43963.1	2
105	HL_72964.1	2
106	HL_80557.1	2
107	HL_05139.1	2
108	HL_25798.1	2
109	HL_57777.1	2
110	HL_77837.1	2
111	HL_86601.1	2
112	HL_27215.1	2
113	HL_45746.1	2
114	HL_58311.1	2
115	HL_65376.1	2
116	HL_00194.1	1
117	HL_12650.1	1
118	HL_16981.1	1
119	HL_22746.1	1
120	HL_27237.1	1
121	HL_30429.1	1
122	HL_32622.1	1
123	HL_50137.1	1
124	HL_58556.1	1
125	HL_78191.1	1
126	HL_95197.1	1
127	HL_06089.1	1
128	HL_20143.1	1
129	HL_22931.1	1
130	HL_27541.1	1
131	HL_35330.1	1
132	HL_38429.1	1
133	HL_42658.1	1
134	HL_51930.1	1
135	HL_66291.1	1
136	HL_81949.1	1
137	HL_84126.1	1
138	HL_95472.1	1
139	HL_00570.1	1
140	HL_04298.1	1
141	HL_10523.1	1
142	HL_17951.1	1
143	HL_20316.1	1
144	HL_23141.1	1
145	HL_29052.1	1
146	HL_35758.1	1
147	HL_47810.1	1
148	HL_52064.1	1
149	HL_72210.1	1
150	HL_79880.1	1
151	HL_24282.1	1
152	HL_36211.1	1
153	HL_40866.1	1
154	HL_43598.1	1
155	HL_55766.1	1
156	HL_61040.1	1
157	HL_01504.1	1
158	HL_04630.1	1
159	HL_12139.1	1
160	HL_24618.1	1
161	HL_36252.1	1
162	HL_48426.1	1
163	HL_56663.1	1
164	HL_83094.1	1
165	HL_85273.1	1
166	HL_92905.1	1
167	HL_96740.1	1
168	HL_12242.1	1
169	HL_14467.1	1
170	HL_18288.1	1
171	HL_29503.1	1
172	HL_49035.1	1
173	HL_54040.1	1
174	HL_73827.1	1
175	HL_77783.1	1
176	HL_83277.1	1
177	HL_98456.1	1
178	HL_05228.1	1
179	HL_06589.1	1
180	HL_12468.1	1
181	HL_14885.1	1
182	HL_22711.1	1
183	HL_29962.1	1
184	HL_37522.1	1
185	HL_41493.1	1
186	HL_62590.1	1
187	HL_75141.1	1
188	HL_80822.1	1
189	HL_99458.1	1
190	HL_03228.1	1
191	HL_12532.1	1
192	HL_15569.1	1
193	HL_22719.1	1
194	HL_30310.1	1
195	HL_37768.1	1
196	HL_42437.1	1
197	HL_54304.1	1
198	HL_70011.1	1
199	HL_80843.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_67042.1	219
2	HL_72498.1	56
3	HL_39895.1	33
4	HL_18781.1	21	Double sheared (tSH) with U-turn
5	HL_52574.1	15	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6	HL_97270.1	15	T-loops with 1 bulged base
7	HL_91226.1	15
8	HL_48039.1	11	MS2 virus RNA Hairpin
9	HL_74465.1	11	tRNA Anti-Codon loop
10	HL_80459.1	11
11	HL_46175.1	10	16S helix 23 and 24 hairpin loops
12	HL_49036.1	10	GNRA with one bulged base
13	HL_56824.1	10	LSU Helix 60A. LSU Helix 63A.
14	HL_75759.1	10	LSU: Part of IL/3WJ between H55 and H56.
15	HL_28436.1	9
16	HL_17723.1	9	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
17	HL_87844.1	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18	HL_82294.1	8
19	HL_11547.1	8	LSU Helix 80 (H80) P-site Hairpin Loop.
20	HL_68081.1	8
21	HL_15603.1	8	U1A protein-binding Hairpin Loop.
22	HL_24544.1	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23	HL_33402.1	7	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
24	HL_01926.1	7	LSU Helix 71 (H71) Hairpin Loop.
25	HL_34027.1	7	5S Loop C - Upper part of Hairpin Loop.
26	HL_70420.1	6	LSU Helix 97 Hairpin loop
27	HL_39872.1	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28	HL_34108.1	6	LSU Helix 37 (H37) Hairpin Loop.
29	HL_18156.1	6	LSU Helix 72 (H72) Hairpin Loop
30	HL_75579.1	6
31	HL_87136.1	6	LSU Helix 39A Hairpin loop
32	HL_41833.1	6	LSU Helix 81 (H81) Hairpin Loop
33	HL_42677.1	6
34	HL_46489.1	6	LSU H89 Hairpin Loop
35	HL_11509.1	6	LSU Helix 6 (H6) Hairpin Loop.
36	HL_39942.1	6	LSU Helix 91 (H91) Hairpin Loop
37	HL_06643.1	5	tRNA D-loop. Sec tRNA
38	HL_88311.1	5	LSU Helix 35 (H35) Hairpin Loop
39	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
40	HL_19261.1	5	SSU Central Pseudoknot (forms helix 2)
41	HL_12811.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
42	HL_72543.1	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
43	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
45	HL_72273.1	5	tRNA D-loop
46	HL_62881.1	4	RNase P Structured Hairpin Loop
47	HL_95423.1	4	UNCG-like. cWW Closing pair.
48	HL_64543.1	4	SSU Helix 31 (h31) Hairpin Loop
49	HL_08382.1	4
50	HL_62228.1	4	LSU Helix 35A (H35A) Hairpin Loop
51	HL_48116.1	4	GNRA-like with 5'-stacking of first unpaired base.
52	HL_98523.1	4	GNRA-like. Closed by tSH UC.
53	HL_29831.1	4	GNRA-like with bulged base.
54	HL_98833.1	3
55	HL_82253.1	3
56	HL_76036.1	3	LSU Helix 8 (H8) Hairpin Loop
57	HL_25124.1	3	tSW GA closed tetraloops
58	HL_20739.1	3
59	HL_27658.1	3
60	HL_78361.1	3
61	HL_54751.1	3
62	HL_32644.1	3	LSU Helix 69 (H69) Hairpin Loop
63	HL_41827.1	3
64	HL_53664.1	3	Double tSH (double sheared) with bulged base
65	HL_90579.1	3
66	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
67	HL_23182.1	3
68	HL_64371.1	3
69	HL_73023.1	3	Two base, cross-stacked hairpin loop
70	HL_16770.1	2
71	HL_19905.1	2
72	HL_81241.1	2
73	HL_76766.1	2
74	HL_61547.1	2
75	HL_08091.1	2
76	HL_26057.1	2
77	HL_76014.1	2
78	HL_85369.1	2
79	HL_20857.1	2
80	HL_87554.1	2
81	HL_63823.1	2
82	HL_56859.1	2
83	HL_70459.1	2
84	HL_10832.1	2
85	HL_24711.1	2
86	HL_42553.1	2
87	HL_57014.1	2
88	HL_76105.1	2
89	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
90	HL_27809.1	2
91	HL_70106.1	2	LSU Helix 10 (H10) Hairpin E.coli
92	HL_94578.1	2
93	HL_33451.1	2
94	HL_05797.1	2
95	HL_03791.1	2
96	HL_99633.1	2
97	HL_06122.1	2
98	HL_49210.1	2
99	HL_67692.1	2
100	HL_44467.1	2
101	HL_96915.1	2
102	HL_23290.1	2
103	HL_14013.1	2
104	HL_49267.1	2
105	HL_23522.1	1
106	HL_58149.1	1
107	HL_65071.1	1
108	HL_58601.1	1
109	HL_34440.1	1
110	HL_12706.1	1
111	HL_67761.1	1
112	HL_53015.1	1
113	HL_25175.1	1
114	HL_90102.1	1	Kink-turn-like Hairpin Loop
115	HL_82288.1	1
116	HL_39922.1	1
117	HL_30128.1	1
118	HL_87223.1	1
119	HL_02479.1	1
120	HL_68579.1	1
121	HL_70912.1	1
122	HL_13786.1	1
123	HL_95716.1	1
124	HL_36842.1	1
125	HL_55202.1	1	U2B"-U2A" binding hairpin loop
126	HL_93567.1	1
127	HL_59604.1	1
128	HL_03431.1	1
129	HL_68435.1	1
130	HL_16860.1	1
131	HL_62970.1	1
132	HL_04194.1	1
133	HL_97971.1	1
134	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
135	HL_56775.1	1
136	HL_07315.1	1
137	HL_35004.1	1
138	HL_81780.1	1
139	HL_58223.1	1
140	HL_85753.1	1
141	HL_62880.1	1
142	HL_03805.1	1
143	HL_78228.1	1
144	HL_35200.1	1
145	HL_97784.1	1
146	HL_81661.1	1	tRNA D-loop
147	HL_35865.1	1
148	HL_58786.1	1
149	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
150	HL_44522.1	1
151	HL_57843.1	1
152	HL_67000.1	1
153	HL_96192.1	1
154	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
155	HL_75850.1	1
156	HL_39486.1	1
157	HL_66900.1	1
158	HL_55543.1	1
159	HL_15771.1	1
160	HL_39422.1	1
161	HL_88960.1	1
162	HL_44390.1	1
163	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
164	HL_33277.1	1
165	HL_10116.1	1	Kink-turn-like Hairpin Loop
166	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
167	HL_66090.1	1
168	HL_99779.1	1
169	HL_37962.1	1
170	HL_63411.1	1
171	HL_05113.1	1
172	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
173	HL_56809.1	1
174	HL_63304.1	1
175	HL_47337.1	1
176	HL_66467.1	1
177	HL_60420.1	1
178	HL_27831.1	1
179	HL_45411.1	1
180	HL_00721.1	1
181	HL_42969.1	1
182	HL_27397.1	1
183	HL_27819.1	1
184	HL_00090.1	1
185	HL_55272.1	1
186	HL_78420.1	1
187	HL_68733.1	1	LSU Yeast Hairpin Loop
188	HL_69403.1	1	GNRA-like

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