Changes in PDB files used for clustering

Release 1.10 has 224 PDB files, release 1.11 has 224 PDB files, 224 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 1.10 has 253 motif groups, release 1.11 has 253 motif groups, 253 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.10, 0 groups are only in release 1.11.

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_67042.10229GNRA Hairpin motifs
2HL_72498.1266T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.420Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_97270.315T-loops with 1 bulged base
7HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_74465.513tRNA Anti-Codon loop
9HL_49036.312GNRA with one bulged base
10HL_27271.212LSU Helix 96 (H96) Hairpin Loop
11HL_48039.211MS2 virus RNA Hairpin
12HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
13HL_56824.210LSU Helix 60A. LSU Helix 63A.
14HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
15HL_68081.310LSU Helix 20 Hairpin loop
16HL_46175.21016S helix 23 and 24 hairpin loops
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_80459.39
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_15603.18U1A protein-binding Hairpin Loop.
21HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_34027.285S Loop C - Upper part of Hairpin Loop.
23HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
24HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
25HL_42677.27
26HL_46489.26LSU H89 Hairpin Loop
27HL_57514.26Two base, cross-stacked hairpin loop
28HL_39942.26LSU Helix 91 (H91) Hairpin Loop
29HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
30HL_70420.26LSU Helix 97 Hairpin loop
31HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
32HL_18156.26LSU Helix 72 (H72) Hairpin Loop
33HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
34HL_75579.26
35HL_87136.26LSU Helix 39A Hairpin loop
36HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
37HL_41833.26LSU Helix 81 (H81) Hairpin Loop
38HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
40HL_45018.35Hairpin-Hairpin Interacting HL
41HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
42HL_88311.25LSU Helix 35 (H35) Hairpin Loop
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
46HL_06643.25tRNA D-loop. Sec tRNA
47HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
48HL_72273.15tRNA D-loop
49HL_47784.24SSU Central Pseudoknot (forms helix 2)
50HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
51HL_11376.14LSU Helix 8 (H8) Hairpin Loop
52HL_98523.24GNRA-like. Closed by tSH UC.
53HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
54HL_64543.24SSU Helix 31 (h31) Hairpin Loop
55HL_25124.24tSW GA closed tetraloops
56HL_86115.14
57HL_62881.14RNase P Structured Hairpin Loop
58HL_29831.14GNRA-like with bulged base.
59HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
60HL_76036.33LSU Helix 8 (H8) Hairpin Loop
61HL_90579.33LSU Helix 69 (H69) Hairpin Loop
62HL_06997.23
63HL_13707.23cSH AA Platform containing Hairpin Loop
64HL_19221.23
65HL_41827.13
66HL_98833.33
67HL_74686.13SSU Central Pseudoknot (forms helix 2)
68HL_27429.33
69HL_76766.43
70HL_78361.13
71HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
72HL_58083.23
73HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
74HL_80492.23tRNA D-loop
75HL_08382.23
76HL_42077.23LSU Helix 28 (H28) Hairpin Loop
77HL_23182.13
78HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
79HL_35619.23
80HL_68697.23
81HL_19399.12
82HL_74559.12Two base, cross-stacked hairpin loop
83HL_90542.12
84HL_63941.12
85HL_24711.12
86HL_49210.12
87HL_94578.12
88HL_18587.12
89HL_62967.12
90HL_54751.22
91HL_91693.12
92HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
93HL_23290.12
94HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
95HL_64371.22
96HL_93771.12tRNA T-loop distorted by RS binding
97HL_74505.12
98HL_24473.32tRNA D-loop
99HL_42094.12
100HL_05361.12
101HL_99633.12
102HL_06122.12
103HL_84353.12
104HL_65924.12
105HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
106HL_17790.12UNCG-like. cWW Closing pair.
107HL_26495.12
108HL_21545.12LSU Helix 96 (H96) Hairpin Loop
109HL_86398.12
110HL_96915.12
111HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
112HL_16770.12
113HL_38130.22
114HL_42553.12
115HL_50312.12
116HL_19528.12
117HL_87554.12
118HL_91872.12
119HL_65249.12
120HL_33451.12
121HL_32644.22LSU Helix 69 (H69) Hairpin Loop
122HL_98577.12
123HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
124HL_23129.12
125HL_60200.12
126HL_59610.11
127HL_56775.11
128HL_30128.11
129HL_48480.11
130HL_78507.11
131HL_58223.11
132HL_58601.11
133HL_88960.11
134HL_44390.11
135HL_67000.11
136HL_62880.11
137HL_04194.11
138HL_93530.11
139HL_19452.11tRNA D-loop
140HL_59182.11
141HL_77692.11tRNA D-loop
142HL_93567.11
143HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
144HL_60203.11
145HL_26579.11
146HL_66877.11cSH GU/cWS double platform, intercalation site
147HL_56809.11
148HL_93263.11
149HL_95716.11
150HL_82243.11
151HL_10116.11Kink-turn-like Hairpin Loop
152HL_73465.11
153HL_45411.11
154HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
155HL_76585.11
156HL_87223.11
157HL_44522.11
158HL_27397.11
159HL_07915.11
160HL_00090.11
161HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
162HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
163HL_78228.11
164HL_97971.11
165HL_69403.11GNRA-like
166HL_46570.11
167HL_01418.11
168HL_29196.11
169HL_52116.11
170HL_59604.11
171HL_97499.11
172HL_65071.11
173HL_39422.11
174HL_84289.11
175HL_34440.11
176HL_27819.11
177HL_67761.11
178HL_63304.11
179HL_75850.11
180HL_35200.11
181HL_82288.11
182HL_83865.11
183HL_59225.11
184HL_73972.11
185HL_53789.11
186HL_25195.11
187HL_37962.11
188HL_68579.11
189HL_12706.11
190HL_13786.11
191HL_55272.11
192HL_47337.11
193HL_39486.11
194HL_36842.11
195HL_23195.11
196HL_30008.11
197HL_84768.11
198HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
199HL_24707.11
200HL_28676.11
201HL_57217.11cHS platform Intercalation Site
202HL_52540.11
203HL_42969.11
204HL_79902.11
205HL_70912.11
206HL_53015.11
207HL_78420.11
208HL_33277.11
209HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
210HL_42345.11
211HL_38138.11
212HL_25197.11
213HL_20806.11
214HL_95049.11Two base, cross-stacked hairpin loop
215HL_84888.11T-loop like but without tWH UA
216HL_57843.11
217HL_03785.11LSU Helix 8 (H8) Hairpin Loop
218HL_25175.11
219HL_68733.11LSU Yeast Hairpin Loop
220HL_66467.11
221HL_99207.11Tetrahymena LSU hairpin poorly modeled
222HL_17537.11
223HL_96994.11
224HL_55202.11U2B"-U2A" binding hairpin loop
225HL_33640.11
226HL_65802.11
227HL_35865.11
228HL_19226.11
229HL_68435.11
230HL_19132.11
231HL_62970.11
232HL_76679.11
233HL_90102.11Kink-turn-like Hairpin Loop
234HL_97784.11
235HL_85018.11
236HL_24108.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription