Changes in PDB files used for clustering

Release 0.7 has 202 PDB files, release 0.8 has 203 PDB files, 202 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_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.115T-loops with 1 bulged base
8HL_74465.111tRNA Anti-Codon loop
9HL_48039.111MS2 virus RNA Hairpin
10HL_80459.111
11HL_68081.210LSU Helix 20 Hairpin loop
12HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
13HL_46175.11016S helix 23 and 24 hairpin loops
14HL_49036.110GNRA with one bulged base
15HL_56824.110LSU Helix 60A. LSU Helix 63A.
16HL_28436.29LSU Helix 96 (H96) Hairpin Loop
17HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
18HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_82294.28SSU Helix 37 (h37) Hairpin loop.
20HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_15603.18U1A protein-binding Hairpin Loop.
22HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_34027.175S Loop C - Upper part of Hairpin Loop.
24HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
25HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
26HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_42677.16
28HL_70420.16LSU Helix 97 Hairpin loop
29HL_87136.16LSU Helix 39A Hairpin loop
30HL_39942.16LSU Helix 91 (H91) Hairpin Loop
31HL_75579.16
32HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
33HL_41833.16LSU Helix 81 (H81) Hairpin Loop
34HL_18156.16LSU Helix 72 (H72) Hairpin Loop
35HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
36HL_46489.16LSU H89 Hairpin Loop
37HL_06643.15tRNA D-loop. Sec tRNA
38HL_19261.15SSU Central Pseudoknot (forms helix 2)
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
41HL_72273.15tRNA D-loop
42HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
43HL_88311.15LSU Helix 35 (H35) Hairpin Loop
44HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
45HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
46HL_95423.14UNCG-like. cWW Closing pair.
47HL_98523.14GNRA-like. Closed by tSH UC.
48HL_29831.14GNRA-like with bulged base.
49HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
50HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
51HL_64543.14SSU Helix 31 (h31) Hairpin Loop
52HL_62881.14RNase P Structured Hairpin Loop
53HL_19221.23
54HL_25124.13tSW GA closed tetraloops
55HL_46794.23
56HL_80492.23tRNA D-loop
57HL_23182.13
58HL_42687.23
59HL_54751.13
60HL_90579.13
61HL_78361.13
62HL_08382.23
63HL_13707.23cSH AA Platform containing Hairpin Loop
64HL_41827.13
65HL_61547.23
66HL_98833.13
67HL_58083.23
68HL_64371.13
69HL_20739.13
70HL_32644.13LSU Helix 69 (H69) Hairpin Loop
71HL_42077.23LSU Helix 28 (H28) Hairpin Loop
72HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
73HL_76036.13LSU Helix 8 (H8) Hairpin Loop
74HL_53664.13Double tSH (double sheared) with bulged base
75HL_82253.13
76HL_27429.23
77HL_73023.13Two base, cross-stacked hairpin loop
78HL_06312.12
79HL_12595.12
80HL_16770.12
81HL_22614.12
82HL_33451.12
83HL_49210.12
84HL_57014.12
85HL_65924.12
86HL_77555.12
87HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
88HL_46981.12
89HL_49267.12
90HL_70459.12
91HL_75575.12
92HL_81555.12
93HL_03791.12
94HL_19399.12
95HL_23290.12
96HL_98577.12
97HL_38130.22
98HL_57904.12
99HL_63823.12
100HL_81752.12
101HL_84353.12
102HL_87554.12
103HL_93015.12
104HL_05361.12
105HL_19905.12
106HL_24473.32tRNA D-loop
107HL_26057.12
108HL_68697.12
109HL_96915.12
110HL_05510.12
111HL_14013.12
112HL_99633.12
113HL_05797.12
114HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
115HL_76105.12
116HL_06122.12
117HL_24711.12
118HL_42553.12
119HL_53753.12
120HL_67692.12
121HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
122HL_76766.12
123HL_94578.12
124HL_02479.11
125HL_27819.11
126HL_35865.11
127HL_53789.11
128HL_59604.11
129HL_63304.11
130HL_67761.11
131HL_90365.115S rRNA Loop C from D.radiodurans
132HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
133HL_97971.11
134HL_03431.11
135HL_12706.11
136HL_17468.11
137HL_25175.11
138HL_27831.11
139HL_33524.11tRNA T-loop distorted by RS binding
140HL_36842.11
141HL_57217.11cHS platform Intercalation Site
142HL_59610.11
143HL_63411.11
144HL_78228.11
145HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
146HL_07315.11
147HL_17537.11
148HL_25195.11
149HL_33640.11
150HL_37962.11
151HL_42969.11
152HL_47337.11
153HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
154HL_55202.11U2B"-U2A" binding hairpin loop
155HL_57843.11
156HL_61061.11
157HL_63690.11
158HL_66467.11
159HL_68435.11
160HL_70912.11
161HL_81661.11tRNA D-loop
162HL_84289.11
163HL_87223.11
164HL_95716.11
165HL_04194.11
166HL_19452.11tRNA D-loop
167HL_23522.11
168HL_25197.11
169HL_44390.11
170HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
171HL_55272.11
172HL_66877.11cSH GU/cWS double platform, intercalation site
173HL_68579.11
174HL_71607.11
175HL_78420.11
176HL_96192.11
177HL_00090.11
178HL_10116.11Kink-turn-like Hairpin Loop
179HL_13786.11
180HL_18011.11
181HL_30128.11
182HL_38138.11
183HL_44522.11
184HL_55543.11
185HL_66900.11
186HL_75850.11
187HL_78507.11
188HL_81780.11
189HL_84888.11T-loop like but without tWH UA
190HL_93206.11
191HL_99207.11Tetrahymena LSU hairpin poorly modeled
192HL_00238.11
193HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
194HL_26579.11
195HL_34440.11
196HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
197HL_45411.11
198HL_53015.11
199HL_56775.11
200HL_58223.11
201HL_62880.11
202HL_67000.11
203HL_68733.11LSU Yeast Hairpin Loop
204HL_82243.11
205HL_85018.11
206HL_93567.11
207HL_20806.11
208HL_24707.11
209HL_27397.11
210HL_33277.11
211HL_35004.11
212HL_39422.11
213HL_48480.11
214HL_56809.11
215HL_58601.11
216HL_65071.11
217HL_69403.11GNRA-like
218HL_79902.11
219HL_88960.11
220HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
221HL_97499.11
222HL_01987.11
223HL_15771.11
224HL_19132.11
225HL_20914.11
226HL_35200.11
227HL_39486.11
228HL_58786.11
229HL_62970.11
230HL_65802.11
231HL_82288.11
232HL_85753.11
233HL_90102.11Kink-turn-like Hairpin Loop
234HL_97784.11

Updated motif groups

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

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription