Changes in PDB files used for clustering

Release 0.5 has 206 PDB files, release 0.6 has 207 PDB files, 203 of them are identical.

3 equivalence classes changed representatives: 3U4M3UMY, 3G784FAW, 2FK64GCW.

1 new structures in release 0.6: 4FY3.

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 0.5 has 247 motif groups, release 0.6 has 245 motif groups, 227 of them are identical.

4 motif groups were updated, 16 groups are present only in release 0.5, 14 groups are only in release 0.6.

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_18781.121Double sheared (tSH) with U-turn
2HL_91226.217Kissing Hairpin motif
3HL_97270.115T-loops with 1 bulged base
4HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
5HL_74465.111tRNA Anti-Codon loop
6HL_80459.111
7HL_48039.111MS2 virus RNA Hairpin
8HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
9HL_49036.110GNRA with one bulged base
10HL_56824.110LSU Helix 60A. LSU Helix 63A.
11HL_46175.11016S helix 23 and 24 hairpin loops
12HL_68081.210LSU Helix 20 Hairpin loop
13HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
14HL_28436.29LSU Helix 96 (H96) Hairpin Loop
15HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_82294.28SSU Helix 37 (h37) Hairpin loop.
19HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
21HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
22HL_34027.175S Loop C - Upper part of Hairpin Loop.
23HL_46489.16LSU H89 Hairpin Loop
24HL_39942.16LSU Helix 91 (H91) Hairpin Loop
25HL_70420.16LSU Helix 97 Hairpin loop
26HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
27HL_18156.16LSU Helix 72 (H72) Hairpin Loop
28HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
29HL_75579.16
30HL_87136.16LSU Helix 39A Hairpin loop
31HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
32HL_41833.16LSU Helix 81 (H81) Hairpin Loop
33HL_42677.16
34HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
35HL_72273.15tRNA D-loop
36HL_88311.15LSU Helix 35 (H35) Hairpin Loop
37HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_19261.15SSU Central Pseudoknot (forms helix 2)
40HL_06643.15tRNA D-loop. Sec tRNA
41HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
42HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
43HL_08382.14
44HL_98523.14GNRA-like. Closed by tSH UC.
45HL_29831.14GNRA-like with bulged base.
46HL_45018.24
47HL_95423.14UNCG-like. cWW Closing pair.
48HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
49HL_64543.14SSU Helix 31 (h31) Hairpin Loop
50HL_62881.14RNase P Structured Hairpin Loop
51HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
52HL_20739.13
53HL_46794.23
54HL_80492.23tRNA D-loop
55HL_27429.23
56HL_78361.13
57HL_53664.13Double tSH (double sheared) with bulged base
58HL_19221.23
59HL_32644.13LSU Helix 69 (H69) Hairpin Loop
60HL_13707.23cSH AA Platform containing Hairpin Loop
61HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
62HL_54751.13
63HL_42687.23
64HL_58083.23
65HL_82253.13
66HL_64371.13
67HL_73023.13Two base, cross-stacked hairpin loop
68HL_98833.13
69HL_90579.13
70HL_41827.13
71HL_42077.23LSU Helix 28 (H28) Hairpin Loop
72HL_23182.13
73HL_76036.13LSU Helix 8 (H8) Hairpin Loop
74HL_25124.13tSW GA closed tetraloops
75HL_65924.12
76HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
77HL_42553.12
78HL_57014.12
79HL_05510.12
80HL_44467.12
81HL_49210.12
82HL_19905.12
83HL_81555.12
84HL_05797.12
85HL_63823.12
86HL_24711.12
87HL_23290.12
88HL_94578.12
89HL_33451.12
90HL_14013.12
91HL_76105.12
92HL_76766.12
93HL_06122.12
94HL_24473.32tRNA D-loop
95HL_46981.12
96HL_88640.12
97HL_19399.12
98HL_67692.12
99HL_26057.12
100HL_16770.12
101HL_57904.12
102HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
103HL_87554.12
104HL_05361.12
105HL_49267.12
106HL_98577.12
107HL_70459.12
108HL_99633.12
109HL_96915.12
110HL_38130.22
111HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
112HL_03791.12
113HL_17008.11Nova-2 KH3 domain binding hairpin
114HL_23522.11
115HL_27831.11
116HL_59604.11
117HL_37962.11
118HL_93206.11
119HL_44522.11
120HL_84289.11
121HL_27397.11
122HL_56809.11
123HL_63304.11
124HL_25175.11
125HL_95716.11
126HL_82288.11
127HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
128HL_56775.11
129HL_48480.11
130HL_57217.11cHS platform Intercalation Site
131HL_81780.11
132HL_90365.115S rRNA Loop C from D.radiodurans
133HL_39422.11
134HL_34440.11
135HL_27819.11
136HL_00090.11
137HL_55272.11
138HL_97971.11
139HL_36842.11
140HL_33524.11tRNA T-loop distorted by RS binding
141HL_81661.11tRNA D-loop
142HL_17468.11
143HL_30128.11
144HL_20806.11
145HL_20914.11
146HL_05113.11
147HL_79902.11
148HL_30731.11
149HL_12706.11
150HL_67761.11
151HL_53015.11
152HL_78228.11
153HL_35200.11
154HL_99207.11Tetrahymena LSU hairpin poorly modeled
155HL_59610.11
156HL_55543.11
157HL_93567.11
158HL_15771.11
159HL_42969.11
160HL_57843.11
161HL_68579.11
162HL_70912.11
163HL_13786.11
164HL_04194.11
165HL_75850.11
166HL_39486.11
167HL_97784.11
168HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
169HL_45411.11
170HL_99779.11
171HL_78507.11
172HL_87223.11
173HL_00721.11
174HL_63411.11
175HL_45358.11Double hairpin loop based on GGA triple
176HL_84888.11T-loop like but without tWH UA
177HL_19132.11
178HL_91613.11
179HL_62970.11
180HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
181HL_33277.11
182HL_66900.11
183HL_55202.11U2B"-U2A" binding hairpin loop
184HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
185HL_07315.11
186HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
187HL_63690.11
188HL_65071.11
189HL_68435.11
190HL_88960.11
191HL_85753.11
192HL_62880.11
193HL_66467.11
194HL_10116.11Kink-turn-like Hairpin Loop
195HL_24707.11
196HL_53789.11
197HL_25195.11
198HL_02479.11
199HL_61061.11
200HL_58223.11
201HL_58601.11
202HL_66877.11cSH GU/cWS double platform, intercalation site
203HL_67000.11
204HL_96192.11
205HL_47337.11
206HL_68733.11LSU Yeast Hairpin Loop
207HL_82243.11
208HL_85018.11
209HL_38898.11
210HL_38138.11
211HL_33640.11
212HL_65802.11
213HL_35865.11
214HL_25197.11
215HL_58786.11
216HL_97499.11
217HL_35004.11
218HL_03431.11
219HL_00238.11
220HL_26579.11
221HL_66880.11
222HL_44390.11
223HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
224HL_78420.11
225HL_90102.11Kink-turn-like Hairpin Loop
226HL_69403.11GNRA-like
227HL_98233.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.3222GNRA Hairpin motifs
2HL_72498.462T-loops with two bulged bases
3HL_39895.334UNCG Hairpin motifs
4HL_61547.23

Removed motif groups

Added motif groups

#Motif idInstancesDescription
1HL_81752.12
2HL_84353.12
3HL_93015.12
4HL_53753.12
5HL_68697.12
6HL_06312.12
7HL_75575.12
8HL_12595.12
9HL_77555.12
10HL_17537.11
11HL_19452.11tRNA D-loop
12HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
13HL_01987.11
14HL_71607.11