Changes in PDB files used for clustering

Release 1.3 has 211 PDB files, release 1.4 has 211 PDB files, 211 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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 1.3 has 256 motif groups, release 1.4 has 256 motif groups, 256 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_67042.7227GNRA Hairpin motifs
2HL_72498.863T-loops with two bulged bases
3HL_39895.535UNCG Hairpin motifs
4HL_18781.220Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.215T-loops with 1 bulged base
8HL_74465.212tRNA Anti-Codon loop
9HL_49036.211GNRA with one bulged base
10HL_48039.111MS2 virus RNA Hairpin
11HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_68081.310LSU Helix 20 Hairpin loop
15HL_80459.210
16HL_46175.11016S helix 23 and 24 hairpin loops
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_28436.39LSU Helix 96 (H96) Hairpin Loop
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_82294.28SSU Helix 37 (h37) Hairpin loop.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
24HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_46489.26LSU H89 Hairpin Loop
26HL_39942.26LSU Helix 91 (H91) Hairpin Loop
27HL_42677.16
28HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
29HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
30HL_70420.26LSU Helix 97 Hairpin loop
31HL_75579.26
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_18156.26LSU Helix 72 (H72) Hairpin Loop
34HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
36HL_41833.26LSU Helix 81 (H81) Hairpin Loop
37HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
38HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
39HL_06643.25tRNA D-loop. Sec tRNA
40HL_88311.25LSU Helix 35 (H35) Hairpin Loop
41HL_45018.35Hairpin-Hairpin Interacting HL
42HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
43HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
44HL_57514.15Two base, cross-stacked hairpin loop
45HL_72273.15tRNA D-loop
46HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
47HL_47784.14SSU Central Pseudoknot (forms helix 2)
48HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
49HL_64543.14SSU Helix 31 (h31) Hairpin Loop
50HL_98523.14GNRA-like. Closed by tSH UC.
51HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
52HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
53HL_62881.14RNase P Structured Hairpin Loop
54HL_18798.14UNCG-like. cWW Closing pair.
55HL_61547.34
56HL_29831.14GNRA-like with bulged base.
57HL_78361.13
58HL_82253.23
59HL_80492.23tRNA D-loop
60HL_27429.33
61HL_46794.23
62HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
63HL_54751.13
64HL_13707.23cSH AA Platform containing Hairpin Loop
65HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
66HL_42687.23
67HL_32644.13LSU Helix 69 (H69) Hairpin Loop
68HL_41827.13
69HL_98833.13
70HL_19221.23
71HL_76036.33LSU Helix 8 (H8) Hairpin Loop
72HL_25124.13tSW GA closed tetraloops
73HL_08382.23
74HL_42077.23LSU Helix 28 (H28) Hairpin Loop
75HL_58083.23
76HL_74686.13SSU Central Pseudoknot (forms helix 2)
77HL_90579.23
78HL_23182.13
79HL_60200.12
80HL_24711.12
81HL_42553.12
82HL_76766.12
83HL_87554.12
84HL_81752.12
85HL_77555.12
86HL_58687.12
87HL_06312.12
88HL_26057.12
89HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
90HL_62967.12
91HL_49210.12
92HL_33451.12
93HL_50312.12
94HL_57014.12
95HL_53753.12
96HL_12595.12
97HL_23290.12
98HL_94578.12
99HL_98577.12
100HL_03791.12
101HL_99633.12
102HL_96915.12
103HL_45440.12
104HL_06122.12
105HL_57904.12
106HL_24473.32tRNA D-loop
107HL_97512.12LSU Helix 8 (H8) Hairpin Loop
108HL_19399.12
109HL_68697.12
110HL_84353.12
111HL_65924.12
112HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
113HL_05361.12
114HL_67692.12
115HL_16770.12
116HL_38130.22
117HL_67367.12
118HL_64371.22
119HL_75575.12
120HL_26495.12
121HL_68579.11
122HL_70912.11
123HL_62970.11
124HL_80746.11
125HL_97971.11
126HL_82243.11
127HL_10116.11Kink-turn-like Hairpin Loop
128HL_16118.11
129HL_81295.11UNCG-like. cWW Closing pair.
130HL_59610.11
131HL_65802.11
132HL_35865.11
133HL_25197.11
134HL_37962.11
135HL_79902.11
136HL_29084.11
137HL_62880.11
138HL_04194.11
139HL_78228.11
140HL_35200.11
141HL_69403.11GNRA-like
142HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
143HL_30008.11
144HL_55543.11
145HL_77692.11tRNA D-loop
146HL_57217.11cHS platform Intercalation Site
147HL_35004.11
148HL_42969.11
149HL_57843.11
150HL_85753.11
151HL_96192.11
152HL_75850.11
153HL_39486.11
154HL_82288.11
155HL_17537.11
156HL_42345.11
157HL_17468.11
158HL_52393.11Double tSH (double sheared) with bulged base
159HL_30128.11
160HL_48480.11
161HL_20806.11
162HL_95049.11Two base, cross-stacked hairpin loop
163HL_84888.11T-loop like but without tWH UA
164HL_19132.11
165HL_44390.11
166HL_67000.11
167HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
168HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
169HL_33277.11
170HL_36842.11
171HL_85018.11
172HL_96994.11
173HL_33524.11tRNA T-loop distorted by RS binding
174HL_93567.11
175HL_19226.11
176HL_52109.11
177HL_68435.11
178HL_88960.11
179HL_56809.11
180HL_63304.11
181HL_66467.11
182HL_19452.11tRNA D-loop
183HL_24108.11
184HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
185HL_45411.11
186HL_78507.11
187HL_20914.11
188HL_58223.11
189HL_58601.11
190HL_66877.11cSH GU/cWS double platform, intercalation site
191HL_07915.11
192HL_00090.11
193HL_55272.11
194HL_47337.11
195HL_68733.11LSU Yeast Hairpin Loop
196HL_99207.11Tetrahymena LSU hairpin poorly modeled
197HL_73465.11
198HL_59182.11
199HL_38138.11
200HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
201HL_07315.11
202HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
203HL_60203.11
204HL_26579.11
205HL_27397.11
206HL_27819.11
207HL_67761.11
208HL_53015.11
209HL_78420.11
210HL_90102.11Kink-turn-like Hairpin Loop
211HL_93530.11
212HL_97784.11
213HL_31969.11
214HL_34375.11
215HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
216HL_53789.11
217HL_25195.11
218HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
219HL_87223.11
220HL_44522.11
221HL_34440.11
222HL_12706.11
223HL_13786.11
224HL_13105.11
225HL_25175.11
226HL_95716.11
227HL_71607.11
228HL_66900.11
229HL_01418.11
230HL_55202.11U2B"-U2A" binding hairpin loop
231HL_56775.11
232HL_12984.11
233HL_33640.11
234HL_24707.11
235HL_59604.11
236HL_97499.11
237HL_63690.11
238HL_65071.11
239HL_39422.11
240HL_84289.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription