Changes in PDB files used for clustering

Release 1.11 has 225 PDB files, release 1.12 has 227 PDB files, 225 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.12: 4C4W, 4OO8.

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 1.11 has 253 motif groups, release 1.12 has 253 motif groups, 249 of them are identical.

4 motif groups were updated, 0 groups are present only in release 1.11, 0 groups are only in release 1.12.

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_72498.1266T-loops with two bulged bases
2HL_39895.635UNCG Hairpin motifs
3HL_18781.420Double sheared (tSH) with U-turn
4HL_91226.317Kissing Hairpin motif
5HL_97270.315T-loops with 1 bulged base
6HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_74465.513tRNA Anti-Codon loop
8HL_49036.312GNRA with one bulged base
9HL_27271.212LSU Helix 96 (H96) Hairpin Loop
10HL_48039.211MS2 virus RNA Hairpin
11HL_68081.310LSU Helix 20 Hairpin loop
12HL_46175.21016S helix 23 and 24 hairpin loops
13HL_56824.210LSU Helix 60A. LSU Helix 63A.
14HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_42677.27
23HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
24HL_46489.26LSU H89 Hairpin Loop
25HL_39942.26LSU Helix 91 (H91) Hairpin Loop
26HL_57514.26Two base, cross-stacked hairpin loop
27HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
28HL_70420.26LSU Helix 97 Hairpin loop
29HL_18156.26LSU Helix 72 (H72) Hairpin Loop
30HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
31HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
32HL_75579.26
33HL_87136.26LSU Helix 39A Hairpin loop
34HL_41833.26LSU Helix 81 (H81) Hairpin Loop
35HL_72273.15tRNA D-loop
36HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
37HL_45018.35Hairpin-Hairpin Interacting HL
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
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_62228.35LSU Helix 35A (H35A) Hairpin Loop
44HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_29831.14GNRA-like with bulged base.
47HL_98523.24GNRA-like. Closed by tSH UC.
48HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
49HL_11376.14LSU Helix 8 (H8) Hairpin Loop
50HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
51HL_47784.24SSU Central Pseudoknot (forms helix 2)
52HL_64543.24SSU Helix 31 (h31) Hairpin Loop
53HL_25124.24tSW GA closed tetraloops
54HL_86115.14
55HL_62881.14RNase P Structured Hairpin Loop
56HL_80492.23tRNA D-loop
57HL_06997.23
58HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
59HL_42077.23LSU Helix 28 (H28) Hairpin Loop
60HL_23182.13
61HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
62HL_35619.23
63HL_08382.23
64HL_68697.23
65HL_19221.23
66HL_76036.33LSU Helix 8 (H8) Hairpin Loop
67HL_90579.33LSU Helix 69 (H69) Hairpin Loop
68HL_13707.23cSH AA Platform containing Hairpin Loop
69HL_58083.23
70HL_74686.13SSU Central Pseudoknot (forms helix 2)
71HL_41827.13
72HL_98833.33
73HL_27429.33
74HL_76766.43
75HL_78361.13
76HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
77HL_06122.12
78HL_65924.12
79HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
80HL_65249.12
81HL_42553.12
82HL_21545.12LSU Helix 96 (H96) Hairpin Loop
83HL_86398.12
84HL_96915.12
85HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
86HL_84353.12
87HL_33451.12
88HL_50312.12
89HL_19528.12
90HL_87554.12
91HL_91872.12
92HL_16770.12
93HL_49210.12
94HL_32644.22LSU Helix 69 (H69) Hairpin Loop
95HL_98577.12
96HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
97HL_23129.12
98HL_60200.12
99HL_23290.12
100HL_94578.12
101HL_19399.12
102HL_74559.12Two base, cross-stacked hairpin loop
103HL_90542.12
104HL_24711.12
105HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
106HL_24473.32tRNA D-loop
107HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
108HL_18587.12
109HL_62967.12
110HL_63941.12
111HL_54751.22
112HL_91693.12
113HL_42094.12
114HL_05361.12
115HL_64371.22
116HL_74505.12
117HL_17790.12UNCG-like. cWW Closing pair.
118HL_99633.12
119HL_93771.12tRNA T-loop distorted by RS binding
120HL_38130.22
121HL_26495.12
122HL_84768.11
123HL_65802.11
124HL_35865.11
125HL_25197.11
126HL_28676.11
127HL_57217.11cHS platform Intercalation Site
128HL_52540.11
129HL_42969.11
130HL_79902.11
131HL_70912.11
132HL_53015.11
133HL_78420.11
134HL_33277.11
135HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
136HL_59225.11
137HL_38138.11
138HL_33640.11
139HL_20806.11
140HL_95049.11Two base, cross-stacked hairpin loop
141HL_84888.11T-loop like but without tWH UA
142HL_57843.11
143HL_03785.11LSU Helix 8 (H8) Hairpin Loop
144HL_25175.11
145HL_68733.11LSU Yeast Hairpin Loop
146HL_66467.11
147HL_99207.11Tetrahymena LSU hairpin poorly modeled
148HL_17537.11
149HL_99584.11
150HL_29196.11
151HL_30128.11
152HL_48480.11
153HL_99779.11
154HL_19226.11
155HL_68435.11
156HL_19132.11
157HL_62970.11
158HL_76679.11
159HL_90102.11Kink-turn-like Hairpin Loop
160HL_97784.11
161HL_85018.11
162HL_08203.11
163HL_55202.11U2B"-U2A" binding hairpin loop
164HL_59610.11
165HL_56775.11
166HL_77692.11tRNA D-loop
167HL_93567.11
168HL_78507.11
169HL_58223.11
170HL_58601.11
171HL_88960.11
172HL_44390.11
173HL_67000.11
174HL_62880.11
175HL_04194.11
176HL_93530.11
177HL_19452.11tRNA D-loop
178HL_30008.11
179HL_45411.11
180HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
181HL_60203.11
182HL_26579.11
183HL_66877.11cSH GU/cWS double platform, intercalation site
184HL_56809.11
185HL_93263.11
186HL_95716.11
187HL_82243.11
188HL_10116.11Kink-turn-like Hairpin Loop
189HL_73465.11
190HL_42345.11
191HL_52116.11
192HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
193HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
194HL_76585.11
195HL_87223.11
196HL_44522.11
197HL_27397.11
198HL_07915.11
199HL_00090.11
200HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
201HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
202HL_78228.11
203HL_97971.11
204HL_69403.11GNRA-like
205HL_46570.11
206HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
207HL_96994.11
208HL_73972.11
209HL_53789.11
210HL_25195.11
211HL_59604.11
212HL_97499.11
213HL_65071.11
214HL_39422.11
215HL_84289.11
216HL_34440.11
217HL_27819.11
218HL_67761.11
219HL_63304.11
220HL_75850.11
221HL_35200.11
222HL_82288.11
223HL_83865.11
224HL_01418.11
225HL_24108.11
226HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
227HL_24707.11
228HL_37962.11
229HL_05113.11
230HL_68579.11
231HL_12706.11
232HL_13786.11
233HL_55272.11
234HL_47337.11
235HL_39486.11
236HL_36842.11
237HL_23195.11
238HL_20028.11
239HL_59182.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.11231GNRA Hairpin motifs
2HL_75759.411
3HL_15603.29U1A protein-binding Hairpin Loop.
4HL_06643.36tRNA D-loop. Sec tRNA

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription