Changes in PDB files used for clustering

Release 1.11 has 224 PDB files, release 1.12 has 226 PDB files, 224 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_46175.21016S helix 23 and 24 hairpin loops
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_82294.38SSU Helix 37 (h37) Hairpin loop.
22HL_42677.27
23HL_18156.26LSU Helix 72 (H72) Hairpin Loop
24HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_70420.26LSU Helix 97 Hairpin loop
26HL_87136.26LSU Helix 39A Hairpin loop
27HL_46489.26LSU H89 Hairpin Loop
28HL_39942.26LSU Helix 91 (H91) Hairpin Loop
29HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
30HL_57514.26Two base, cross-stacked hairpin loop
31HL_75579.26
32HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
33HL_41833.26LSU Helix 81 (H81) Hairpin Loop
34HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
35HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
36HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
37HL_72273.15tRNA D-loop
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41HL_88311.25LSU Helix 35 (H35) Hairpin Loop
42HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
43HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
44HL_45018.35Hairpin-Hairpin Interacting HL
45HL_64543.24SSU Helix 31 (h31) Hairpin Loop
46HL_62881.14RNase P Structured Hairpin Loop
47HL_29831.14GNRA-like with bulged base.
48HL_98523.24GNRA-like. Closed by tSH UC.
49HL_47784.24SSU Central Pseudoknot (forms helix 2)
50HL_11376.14LSU Helix 8 (H8) Hairpin Loop
51HL_25124.24tSW GA closed tetraloops
52HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53HL_86115.14
54HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
55HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
56HL_35619.23
57HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
58HL_06997.23
59HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
60HL_76766.43
61HL_90579.33LSU Helix 69 (H69) Hairpin Loop
62HL_13707.23cSH AA Platform containing Hairpin Loop
63HL_80492.23tRNA D-loop
64HL_08382.23
65HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
66HL_74686.13SSU Central Pseudoknot (forms helix 2)
67HL_19221.23
68HL_41827.13
69HL_78361.13
70HL_23182.13
71HL_27429.33
72HL_42077.23LSU Helix 28 (H28) Hairpin Loop
73HL_58083.23
74HL_68697.23
75HL_76036.33LSU Helix 8 (H8) Hairpin Loop
76HL_98833.33
77HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
78HL_06122.12
79HL_19528.12
80HL_23290.12
81HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
82HL_86398.12
83HL_90542.12
84HL_93771.12tRNA T-loop distorted by RS binding
85HL_99633.12
86HL_18587.12
87HL_33451.12
88HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
89HL_65249.12
90HL_74505.12
91HL_84353.12
92HL_94578.12
93HL_24473.32tRNA D-loop
94HL_26495.12
95HL_42553.12
96HL_62967.12
97HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
98HL_74559.12Two base, cross-stacked hairpin loop
99HL_21545.12LSU Helix 96 (H96) Hairpin Loop
100HL_49210.12
101HL_87554.12
102HL_91693.12
103HL_16770.12
104HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
105HL_38130.22
106HL_54751.22
107HL_60200.12
108HL_65924.12
109HL_91872.12
110HL_23129.12
111HL_24711.12
112HL_63941.12
113HL_98577.12
114HL_19399.12
115HL_32644.22LSU Helix 69 (H69) Hairpin Loop
116HL_50312.12
117HL_64371.22
118HL_96915.12
119HL_05361.12
120HL_17790.12UNCG-like. cWW Closing pair.
121HL_42094.12
122HL_58601.11
123HL_66877.11cSH GU/cWS double platform, intercalation site
124HL_68733.11LSU Yeast Hairpin Loop
125HL_73972.11
126HL_76585.11
127HL_83865.11
128HL_90102.11Kink-turn-like Hairpin Loop
129HL_93567.11
130HL_96994.11
131HL_99207.11Tetrahymena LSU hairpin poorly modeled
132HL_25195.11
133HL_28676.11
134HL_39486.11
135HL_42345.11
136HL_45411.11
137HL_52540.11
138HL_56775.11
139HL_59182.11
140HL_62880.11
141HL_65071.11
142HL_69403.11GNRA-like
143HL_76679.11
144HL_79902.11
145HL_84289.11
146HL_12706.11
147HL_24108.11
148HL_25197.11
149HL_29196.11
150HL_35865.11
151HL_48480.11
152HL_56809.11
153HL_59225.11
154HL_67000.11
155HL_97499.11
156HL_00090.11
157HL_07915.11
158HL_20806.11
159HL_33640.11
160HL_36842.11
161HL_53015.11
162HL_59604.11
163HL_67761.11
164HL_70912.11
165HL_77692.11tRNA D-loop
166HL_84768.11
167HL_87223.11
168HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
169HL_97784.11
170HL_01418.11
171HL_13786.11
172HL_19132.11
173HL_26579.11
174HL_30008.11
175HL_37962.11
176HL_46570.11
177HL_53789.11
178HL_57217.11cHS platform Intercalation Site
179HL_59610.11
180HL_62970.11
181HL_65802.11
182HL_78228.11
183HL_82243.11
184HL_84888.11T-loop like but without tWH UA
185HL_95049.11Two base, cross-stacked hairpin loop
186HL_97971.11
187HL_10116.11Kink-turn-like Hairpin Loop
188HL_24707.11
189HL_30128.11
190HL_42969.11
191HL_47337.11
192HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
193HL_63304.11
194HL_68435.11
195HL_82288.11
196HL_85018.11
197HL_95716.11
198HL_03785.11LSU Helix 8 (H8) Hairpin Loop
199HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
200HL_17537.11
201HL_19226.11
202HL_27397.11
203HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
204HL_38138.11
205HL_44390.11
206HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
207HL_55202.11U2B"-U2A" binding hairpin loop
208HL_57843.11
209HL_60203.11
210HL_68579.11
211HL_75850.11
212HL_78420.11
213HL_93263.11
214HL_04194.11
215HL_34440.11
216HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
217HL_44522.11
218HL_55272.11
219HL_66467.11
220HL_73465.11
221HL_78507.11
222HL_88960.11
223HL_93530.11
224HL_19452.11tRNA D-loop
225HL_23195.11
226HL_25175.11
227HL_27819.11
228HL_33277.11
229HL_35200.11
230HL_39422.11
231HL_52116.11
232HL_58223.11

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