Changes in PDB files used for clustering

Release 0.7 has 203 PDB files, release 0.8 has 204 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 0.8: 4ATO.

No equivalence class representatives have been obsoleted.

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

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Changes in motif groups

Release 0.7 has 246 motif groups, release 0.8 has 246 motif groups, 245 of them are identical.

1 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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 idInstancesDescription
1HL_67042.3222GNRA Hairpin motifs
2HL_72498.462T-loops with two bulged bases
3HL_39895.334UNCG Hairpin motifs
4HL_18781.121Double sheared (tSH) with U-turn
5HL_91226.217Kissing Hairpin motif
6HL_97270.115T-loops with 1 bulged base
7HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_80459.111
9HL_48039.111MS2 virus RNA Hairpin
10HL_74465.111tRNA Anti-Codon loop
11HL_68081.210LSU Helix 20 Hairpin loop
12HL_46175.11016S helix 23 and 24 hairpin loops
13HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
14HL_49036.110GNRA with one bulged base
15HL_56824.110LSU Helix 60A. LSU Helix 63A.
16HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
17HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_28436.29LSU Helix 96 (H96) Hairpin Loop
19HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_15603.18U1A protein-binding Hairpin Loop.
22HL_82294.28SSU Helix 37 (h37) Hairpin loop.
23HL_34027.175S Loop C - Upper part of Hairpin Loop.
24HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
26HL_42677.16
27HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.16LSU Helix 72 (H72) Hairpin Loop
29HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_75579.16
31HL_87136.16LSU Helix 39A Hairpin loop
32HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
33HL_41833.16LSU Helix 81 (H81) Hairpin Loop
34HL_46489.16LSU H89 Hairpin Loop
35HL_39942.16LSU Helix 91 (H91) Hairpin Loop
36HL_70420.16LSU Helix 97 Hairpin loop
37HL_06643.15tRNA D-loop. Sec tRNA
38HL_72273.15tRNA D-loop
39HL_19261.15SSU Central Pseudoknot (forms helix 2)
40HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
41HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
42HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
43HL_88311.15LSU Helix 35 (H35) Hairpin Loop
44HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
45HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
46HL_62881.14RNase P Structured Hairpin Loop
47HL_29831.14GNRA-like with bulged base.
48HL_95423.14UNCG-like. cWW Closing pair.
49HL_98523.14GNRA-like. Closed by tSH UC.
50HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
51HL_64543.14SSU Helix 31 (h31) Hairpin Loop
52HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
53HL_41827.13
54HL_98833.13
55HL_32644.13LSU Helix 69 (H69) Hairpin Loop
56HL_61547.23
57HL_58083.23
58HL_82253.13
59HL_64371.13
60HL_73023.13Two base, cross-stacked hairpin loop
61HL_08382.23
62HL_42077.23LSU Helix 28 (H28) Hairpin Loop
63HL_20739.13
64HL_23182.13
65HL_76036.13LSU Helix 8 (H8) Hairpin Loop
66HL_90579.13
67HL_80492.23tRNA D-loop
68HL_25124.13tSW GA closed tetraloops
69HL_46794.23
70HL_27429.23
71HL_54751.13
72HL_13707.23cSH AA Platform containing Hairpin Loop
73HL_53664.13Double tSH (double sheared) with bulged base
74HL_78361.13
75HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
76HL_42687.23
77HL_19221.23
78HL_06122.12
79HL_57904.12
80HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
81HL_46981.12
82HL_14013.12
83HL_05797.12
84HL_76105.12
85HL_76766.12
86HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
87HL_68697.12
88HL_84353.12
89HL_65924.12
90HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
91HL_19399.12
92HL_26057.12
93HL_03791.12
94HL_16770.12
95HL_38130.22
96HL_05361.12
97HL_93015.12
98HL_67692.12
99HL_98577.12
100HL_75575.12
101HL_49267.12
102HL_63823.12
103HL_24711.12
104HL_81752.12
105HL_49210.12
106HL_19905.12
107HL_77555.12
108HL_42553.12
109HL_23290.12
110HL_81555.12
111HL_06312.12
112HL_05510.12
113HL_87554.12
114HL_53753.12
115HL_12595.12
116HL_24473.32tRNA D-loop
117HL_94578.12
118HL_33451.12
119HL_22614.12
120HL_57014.12
121HL_70459.12
122HL_99633.12
123HL_96915.12
124HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
125HL_99779.11
126HL_42969.11
127HL_57843.11
128HL_67000.11
129HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
130HL_47337.11
131HL_68733.11LSU Yeast Hairpin Loop
132HL_97784.11
133HL_38138.11
134HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
135HL_07315.11
136HL_45411.11
137HL_78507.11
138HL_20914.11
139HL_15771.11
140HL_84888.11T-loop like but without tWH UA
141HL_19132.11
142HL_44390.11
143HL_63304.11
144HL_78420.11
145HL_90102.11Kink-turn-like Hairpin Loop
146HL_18011.11
147HL_66900.11
148HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
149HL_24707.11
150HL_53789.11
151HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
152HL_63411.11
153HL_68435.11
154HL_88960.11
155HL_56809.11
156HL_00090.11
157HL_55272.11
158HL_25175.11
159HL_95716.11
160HL_71607.11
161HL_10116.11Kink-turn-like Hairpin Loop
162HL_55202.11U2B"-U2A" binding hairpin loop
163HL_56775.11
164HL_33640.11
165HL_65802.11
166HL_35865.11
167HL_25197.11
168HL_58786.11
169HL_25195.11
170HL_87223.11
171HL_65071.11
172HL_58223.11
173HL_58601.11
174HL_66877.11cSH GU/cWS double platform, intercalation site
175HL_27819.11
176HL_67761.11
177HL_53015.11
178HL_97971.11
179HL_82243.11
180HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
181HL_59610.11
182HL_23522.11
183HL_27831.11
184HL_59604.11
185HL_97499.11
186HL_63690.11
187HL_02479.11
188HL_61061.11
189HL_26579.11
190HL_27397.11
191HL_12706.11
192HL_13786.11
193HL_04194.11
194HL_78228.11
195HL_35200.11
196HL_69403.11GNRA-like
197HL_17537.11
198HL_55543.11
199HL_81661.11tRNA D-loop
200HL_37962.11
201HL_03431.11
202HL_00238.11
203HL_44522.11
204HL_84289.11
205HL_34440.11
206HL_70912.11
207HL_62970.11
208HL_01987.11
209HL_75850.11
210HL_39486.11
211HL_82288.11
212HL_85018.11
213HL_17468.11
214HL_30128.11
215HL_48480.11
216HL_57217.11cHS platform Intercalation Site
217HL_35004.11
218HL_93206.11
219HL_39422.11
220HL_68579.11
221HL_62880.11
222HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
223HL_33277.11
224HL_36842.11
225HL_19452.11tRNA D-loop
226HL_33524.11tRNA T-loop distorted by RS binding
227HL_93567.11
228HL_20806.11
229HL_81780.11
230HL_90365.115S rRNA Loop C from D.radiodurans
231HL_05113.11
232HL_79902.11
233HL_85753.11
234HL_96192.11
235HL_66467.11
236HL_99207.11Tetrahymena LSU hairpin poorly modeled

Updated motif groups

#Motif idInstancesDescription
1HL_45018.35Hairpin-Hairpin Interacting HL

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription