Changes in PDB files used for clustering

Release 0.3 has 194 PDB files, release 0.4 has 195 PDB files, 194 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_80459.111
8HL_48039.111MS2 virus RNA Hairpin
9HL_74465.111tRNA Anti-Codon loop
10HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
11HL_56824.110LSU Helix 60A. LSU Helix 63A.
12HL_46175.11016S helix 23 and 24 hairpin loops
13HL_49036.110GNRA with one bulged base
14HL_28436.19
15HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
16HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_68081.18
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_82294.18
22HL_34027.175S Loop C - Upper part of Hairpin Loop.
23HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
24HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_42677.16
26HL_46489.16LSU H89 Hairpin Loop
27HL_75579.16
28HL_70420.16LSU Helix 97 Hairpin loop
29HL_39942.16LSU Helix 91 (H91) Hairpin Loop
30HL_18156.16LSU Helix 72 (H72) Hairpin Loop
31HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
32HL_41833.16LSU Helix 81 (H81) Hairpin Loop
33HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
34HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_87136.16LSU Helix 39A Hairpin loop
36HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
37HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
38HL_88311.15LSU Helix 35 (H35) Hairpin Loop
39HL_72273.15tRNA D-loop
40HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
43HL_06643.15tRNA D-loop. Sec tRNA
44HL_19261.15SSU Central Pseudoknot (forms helix 2)
45HL_95423.14UNCG-like. cWW Closing pair.
46HL_98523.14GNRA-like. Closed by tSH UC.
47HL_08382.14
48HL_29831.14GNRA-like with bulged base.
49HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
50HL_45018.24
51HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
52HL_64543.14SSU Helix 31 (h31) Hairpin Loop
53HL_62881.14RNase P Structured Hairpin Loop
54HL_42687.23
55HL_46794.23
56HL_80492.23tRNA D-loop
57HL_90579.13
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_20739.13
60HL_78361.13
61HL_98833.13
62HL_41827.13
63HL_58083.23
64HL_27429.23
65HL_32644.13LSU Helix 69 (H69) Hairpin Loop
66HL_19221.23
67HL_25124.13tSW GA closed tetraloops
68HL_27658.13
69HL_42077.23LSU Helix 28 (H28) Hairpin Loop
70HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
71HL_53664.13Double tSH (double sheared) with bulged base
72HL_64371.13
73HL_76036.13LSU Helix 8 (H8) Hairpin Loop
74HL_82253.13
75HL_23182.13
76HL_73023.13Two base, cross-stacked hairpin loop
77HL_54751.13
78HL_03791.12
79HL_08091.12
80HL_19905.12
81HL_49210.12
82HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
83HL_24473.32tRNA D-loop
84HL_26057.12
85HL_49267.12
86HL_65924.12
87HL_67692.12
88HL_87554.12
89HL_98577.12
90HL_38130.22
91HL_57904.12
92HL_70459.12
93HL_81241.12
94HL_05510.12
95HL_76014.12
96HL_85369.12
97HL_96915.12
98HL_05797.12
99HL_10832.12
100HL_14013.12
101HL_20857.12
102HL_24711.12
103HL_61547.12
104HL_63823.12
105HL_88640.12
106HL_99633.12
107HL_06122.12
108HL_27809.12
109HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
110HL_56859.12
111HL_76105.12
112HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
113HL_94578.12
114HL_16770.12
115HL_19399.12
116HL_23290.12
117HL_33451.12
118HL_42553.12
119HL_57014.12
120HL_76766.12
121HL_12706.11
122HL_16860.11
123HL_23522.11
124HL_25197.11
125HL_27831.11
126HL_33524.11tRNA T-loop distorted by RS binding
127HL_36842.11
128HL_55202.11U2B"-U2A" binding hairpin loop
129HL_57217.11cHS platform Intercalation Site
130HL_59604.11
131HL_62970.11
132HL_65802.11
133HL_77981.11
134HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
135HL_87223.11
136HL_90365.115S rRNA Loop C from D.radiodurans
137HL_03805.11
138HL_17468.11
139HL_20252.11
140HL_33640.11
141HL_37962.11
142HL_39922.11
143HL_55272.11
144HL_57843.11
145HL_59610.11
146HL_63304.11
147HL_78228.11
148HL_84289.11
149HL_95716.11
150HL_04194.11
151HL_10116.11Kink-turn-like Hairpin Loop
152HL_26579.11
153HL_42969.11
154HL_47337.11
155HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
156HL_55543.11
157HL_60420.11
158HL_63411.11
159HL_66090.11
160HL_67761.11
161HL_75850.11
162HL_84888.11T-loop like but without tWH UA
163HL_96192.11
164HL_00090.11
165HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
166HL_13786.11
167HL_20806.11
168HL_24707.11
169HL_27397.11
170HL_30128.11
171HL_38138.11
172HL_44390.11
173HL_56775.11
174HL_61061.11
175HL_63690.11
176HL_70912.11
177HL_78420.11
178HL_81661.11tRNA D-loop
179HL_93206.11
180HL_99207.11Tetrahymena LSU hairpin poorly modeled
181HL_00238.11
182HL_34440.11
183HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
184HL_44522.11
185HL_53015.11
186HL_56809.11
187HL_58149.11
188HL_66467.11
189HL_68435.11
190HL_76027.11
191HL_78507.11
192HL_81780.11
193HL_93567.11
194HL_10842.11
195HL_20914.11
196HL_33277.11
197HL_35004.11
198HL_39422.11
199HL_58223.11
200HL_66877.11cSH GU/cWS double platform, intercalation site
201HL_68579.11
202HL_85753.11
203HL_88921.11
204HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
205HL_97499.11
206HL_02479.11
207HL_15771.11
208HL_25175.11
209HL_35200.11
210HL_39486.11
211HL_45411.11
212HL_48480.11
213HL_53789.11
214HL_58601.11
215HL_62880.11
216HL_66900.11
217HL_68733.11LSU Yeast Hairpin Loop
218HL_79390.11
219HL_82288.11
220HL_88960.11
221HL_97784.11
222HL_03431.11
223HL_07315.11
224HL_25195.11
225HL_27819.11
226HL_35865.11
227HL_58786.11
228HL_65071.11
229HL_67000.11
230HL_69403.11GNRA-like
231HL_79902.11
232HL_90102.11Kink-turn-like Hairpin Loop
233HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
234HL_97971.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.258

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription