Changes in PDB files used for clustering

Release 0.3 has 199 PDB files, release 0.4 has 200 PDB files, 199 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 0.4: 3VJR.

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

Loading the Sankey diagram...

Changes in motif groups

Release 0.3 has 245 motif groups, release 0.4 has 245 motif groups, 244 of them are identical.

1 motif groups were updated, 0 groups are present only in release 0.3, 0 groups are only in release 0.4.

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_67042.1219
2HL_39895.133
3HL_18781.121Double sheared (tSH) with U-turn
4HL_91226.115
5HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_97270.115T-loops with 1 bulged base
7HL_74465.111tRNA Anti-Codon loop
8HL_80459.111
9HL_48039.111MS2 virus RNA Hairpin
10HL_46175.11016S helix 23 and 24 hairpin loops
11HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
12HL_49036.110GNRA with one bulged base
13HL_56824.110LSU Helix 60A. LSU Helix 63A.
14HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_28436.19
16HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
17HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_15603.18U1A protein-binding Hairpin Loop.
19HL_82294.18
20HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_68081.18
22HL_34027.175S Loop C - Upper part of Hairpin Loop.
23HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
24HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
25HL_46489.16LSU H89 Hairpin Loop
26HL_39942.16LSU Helix 91 (H91) Hairpin Loop
27HL_70420.16LSU Helix 97 Hairpin loop
28HL_42677.16
29HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
30HL_18156.16LSU Helix 72 (H72) Hairpin Loop
31HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
32HL_75579.16
33HL_87136.16LSU Helix 39A Hairpin loop
34HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
35HL_41833.16LSU Helix 81 (H81) Hairpin Loop
36HL_72273.15tRNA D-loop
37HL_19261.15SSU Central Pseudoknot (forms helix 2)
38HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_06643.15tRNA D-loop. Sec tRNA
40HL_88311.15LSU Helix 35 (H35) Hairpin Loop
41HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
42HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
45HL_95423.14UNCG-like. cWW Closing pair.
46HL_98523.14GNRA-like. Closed by tSH UC.
47HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
48HL_64543.14SSU Helix 31 (h31) Hairpin Loop
49HL_45018.24
50HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
51HL_62881.14RNase P Structured Hairpin Loop
52HL_29831.14GNRA-like with bulged base.
53HL_08382.14
54HL_20739.13
55HL_23182.13
56HL_32644.13LSU Helix 69 (H69) Hairpin Loop
57HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
58HL_73023.13Two base, cross-stacked hairpin loop
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_46794.23
61HL_80492.23tRNA D-loop
62HL_27658.13
63HL_54751.13
64HL_42687.23
65HL_53664.13Double tSH (double sheared) with bulged base
66HL_76036.13LSU Helix 8 (H8) Hairpin Loop
67HL_90579.13
68HL_98833.13
69HL_41827.13
70HL_19221.23
71HL_27429.23
72HL_25124.13tSW GA closed tetraloops
73HL_58083.23
74HL_82253.13
75HL_42077.23LSU Helix 28 (H28) Hairpin Loop
76HL_64371.13
77HL_78361.13
78HL_20857.12
79HL_19399.12
80HL_76105.12
81HL_76766.12
82HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
83HL_99633.12
84HL_24711.12
85HL_08091.12
86HL_81241.12
87HL_67692.12
88HL_26057.12
89HL_03791.12
90HL_96915.12
91HL_10832.12
92HL_49210.12
93HL_44467.12
94HL_23290.12
95HL_19905.12
96HL_49267.12
97HL_98577.12
98HL_56859.12
99HL_27809.12
100HL_24473.32tRNA D-loop
101HL_85369.12
102HL_06122.12
103HL_57904.12
104HL_94578.12
105HL_42553.12
106HL_76014.12
107HL_63823.12
108HL_65924.12
109HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
110HL_61547.12
111HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
112HL_33451.12
113HL_57014.12
114HL_05510.12
115HL_87554.12
116HL_16770.12
117HL_38130.22
118HL_88640.12
119HL_14013.12
120HL_05797.12
121HL_70459.12
122HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
123HL_75850.11
124HL_39486.11
125HL_66900.11
126HL_38898.11
127HL_56775.11
128HL_33640.11
129HL_65802.11
130HL_35865.11
131HL_24707.11
132HL_53789.11
133HL_58149.11
134HL_99779.11
135HL_20914.11
136HL_05113.11
137HL_77981.11
138HL_66880.11
139HL_67000.11
140HL_96192.11
141HL_33277.11
142HL_10116.11Kink-turn-like Hairpin Loop
143HL_17008.11Nova-2 KH3 domain binding hairpin
144HL_59610.11
145HL_23522.11
146HL_25197.11
147HL_58786.11
148HL_78507.11
149HL_15771.11
150HL_42969.11
151HL_76027.11
152HL_27397.11
153HL_44390.11
154HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
155HL_47337.11
156HL_66467.11
157HL_55543.11
158HL_81661.11tRNA D-loop
159HL_27831.11
160HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
161HL_87223.11
162HL_00721.11
163HL_63411.11
164HL_45358.11Double hairpin loop based on GGA triple
165HL_84888.11T-loop like but without tWH UA
166HL_88921.11
167HL_34440.11
168HL_56809.11
169HL_63304.11
170HL_78420.11
171HL_68733.11LSU Yeast Hairpin Loop
172HL_69403.11GNRA-like
173HL_17468.11
174HL_79390.11
175HL_25195.11
176HL_63690.11
177HL_65071.11
178HL_68435.11
179HL_30731.11
180HL_27819.11
181HL_00090.11
182HL_55272.11
183HL_25175.11
184HL_90102.11Kink-turn-like Hairpin Loop
185HL_82288.11
186HL_33524.11tRNA T-loop distorted by RS binding
187HL_20252.11
188HL_30128.11
189HL_48480.11
190HL_59604.11
191HL_97499.11
192HL_02479.11
193HL_61061.11
194HL_58223.11
195HL_58601.11
196HL_79902.11
197HL_68579.11
198HL_12706.11
199HL_67761.11
200HL_53015.11
201HL_95716.11
202HL_36842.11
203HL_39922.11
204HL_93567.11
205HL_37962.11
206HL_35004.11
207HL_03431.11
208HL_00238.11
209HL_26579.11
210HL_57843.11
211HL_16860.11
212HL_70912.11
213HL_13786.11
214HL_97971.11
215HL_99207.11Tetrahymena LSU hairpin poorly modeled
216HL_55202.11U2B"-U2A" binding hairpin loop
217HL_60420.11
218HL_38138.11
219HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
220HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
221HL_66090.11
222HL_10842.11
223HL_57217.11cHS platform Intercalation Site
224HL_93206.11
225HL_44522.11
226HL_84289.11
227HL_88960.11
228HL_91613.11
229HL_62970.11
230HL_04194.11
231HL_78228.11
232HL_35200.11
233HL_97784.11
234HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
235HL_07315.11
236HL_45411.11
237HL_20806.11
238HL_81780.11
239HL_90365.115S rRNA Loop C from D.radiodurans
240HL_39422.11
241HL_66877.11cSH GU/cWS double platform, intercalation site
242HL_85753.11
243HL_62880.11
244HL_03805.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.258

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription