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_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_46175.21016S helix 23 and 24 hairpin loops
14HL_56824.210LSU Helix 60A. LSU Helix 63A.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_82294.38SSU Helix 37 (h37) Hairpin loop.
19HL_34027.285S Loop C - Upper part of Hairpin Loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_42677.27
23HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
24HL_70420.26LSU Helix 97 Hairpin loop
25HL_18156.26LSU Helix 72 (H72) Hairpin Loop
26HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
28HL_75579.26
29HL_87136.26LSU Helix 39A Hairpin loop
30HL_41833.26LSU Helix 81 (H81) Hairpin Loop
31HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
32HL_46489.26LSU H89 Hairpin Loop
33HL_57514.26Two base, cross-stacked hairpin loop
34HL_39942.26LSU Helix 91 (H91) Hairpin Loop
35HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
36HL_88311.25LSU Helix 35 (H35) Hairpin Loop
37HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
38HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
39HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
40HL_72273.15tRNA D-loop
41HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_45018.35Hairpin-Hairpin Interacting HL
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_47784.24SSU Central Pseudoknot (forms helix 2)
46HL_64543.24SSU Helix 31 (h31) Hairpin Loop
47HL_86115.14
48HL_62881.14RNase P Structured Hairpin Loop
49HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
50HL_29831.14GNRA-like with bulged base.
51HL_98523.24GNRA-like. Closed by tSH UC.
52HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
53HL_25124.24tSW GA closed tetraloops
54HL_11376.14LSU Helix 8 (H8) Hairpin Loop
55HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
56HL_19221.23
57HL_78361.13
58HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_74686.13SSU Central Pseudoknot (forms helix 2)
61HL_27429.33
62HL_76766.43
63HL_58083.23
64HL_41827.13
65HL_98833.33
66HL_80492.23tRNA D-loop
67HL_68697.23
68HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
69HL_35619.23
70HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
71HL_42077.23LSU Helix 28 (H28) Hairpin Loop
72HL_23182.13
73HL_90579.33LSU Helix 69 (H69) Hairpin Loop
74HL_06997.23
75HL_08382.23
76HL_76036.33LSU Helix 8 (H8) Hairpin Loop
77HL_24711.12
78HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
79HL_24473.32tRNA D-loop
80HL_42094.12
81HL_05361.12
82HL_63941.12
83HL_54751.22
84HL_91693.12
85HL_21545.12LSU Helix 96 (H96) Hairpin Loop
86HL_86398.12
87HL_96915.12
88HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
89HL_74505.12
90HL_17790.12UNCG-like. cWW Closing pair.
91HL_26495.12
92HL_19528.12
93HL_87554.12
94HL_91872.12
95HL_93771.12tRNA T-loop distorted by RS binding
96HL_38130.22
97HL_42553.12
98HL_50312.12
99HL_98577.12
100HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
101HL_23129.12
102HL_60200.12
103HL_06122.12
104HL_65924.12
105HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
106HL_65249.12
107HL_33451.12
108HL_32644.22LSU Helix 69 (H69) Hairpin Loop
109HL_74559.12Two base, cross-stacked hairpin loop
110HL_90542.12
111HL_84353.12
112HL_19399.12
113HL_18587.12
114HL_62967.12
115HL_16770.12
116HL_49210.12
117HL_94578.12
118HL_64371.22
119HL_23290.12
120HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
121HL_99633.12
122HL_59604.11
123HL_97499.11
124HL_65071.11
125HL_39422.11
126HL_68579.11
127HL_12706.11
128HL_13786.11
129HL_55272.11
130HL_47337.11
131HL_39486.11
132HL_36842.11
133HL_23195.11
134HL_30008.11
135HL_52116.11
136HL_53789.11
137HL_25195.11
138HL_37962.11
139HL_42969.11
140HL_79902.11
141HL_70912.11
142HL_53015.11
143HL_78420.11
144HL_33277.11
145HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
146HL_42345.11
147HL_73972.11
148HL_24707.11
149HL_28676.11
150HL_57217.11cHS platform Intercalation Site
151HL_52540.11
152HL_84888.11T-loop like but without tWH UA
153HL_57843.11
154HL_03785.11LSU Helix 8 (H8) Hairpin Loop
155HL_25175.11
156HL_68733.11LSU Yeast Hairpin Loop
157HL_66467.11
158HL_99207.11Tetrahymena LSU hairpin poorly modeled
159HL_17537.11
160HL_96994.11
161HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
162HL_25197.11
163HL_20806.11
164HL_95049.11Two base, cross-stacked hairpin loop
165HL_19132.11
166HL_62970.11
167HL_76679.11
168HL_90102.11Kink-turn-like Hairpin Loop
169HL_97784.11
170HL_85018.11
171HL_24108.11
172HL_84768.11
173HL_65802.11
174HL_35865.11
175HL_19226.11
176HL_68435.11
177HL_58601.11
178HL_88960.11
179HL_44390.11
180HL_67000.11
181HL_62880.11
182HL_04194.11
183HL_93530.11
184HL_19452.11tRNA D-loop
185HL_59182.11
186HL_38138.11
187HL_33640.11
188HL_30128.11
189HL_48480.11
190HL_78507.11
191HL_58223.11
192HL_66877.11cSH GU/cWS double platform, intercalation site
193HL_56809.11
194HL_93263.11
195HL_95716.11
196HL_82243.11
197HL_10116.11Kink-turn-like Hairpin Loop
198HL_73465.11
199HL_93567.11
200HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
201HL_60203.11
202HL_26579.11
203HL_27397.11
204HL_07915.11
205HL_00090.11
206HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
207HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
208HL_78228.11
209HL_97971.11
210HL_69403.11GNRA-like
211HL_46570.11
212HL_01418.11
213HL_29196.11
214HL_55202.11U2B"-U2A" binding hairpin loop
215HL_59610.11
216HL_56775.11
217HL_77692.11tRNA D-loop
218HL_45411.11
219HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
220HL_76585.11
221HL_87223.11
222HL_44522.11
223HL_84289.11
224HL_34440.11
225HL_27819.11
226HL_67761.11
227HL_63304.11
228HL_75850.11
229HL_35200.11
230HL_82288.11
231HL_83865.11
232HL_59225.11

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