Changes in PDB files used for clustering

Release 0.11 has 196 PDB files, release 0.12 has 196 PDB files, 196 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 0.11 has 266 motif groups, release 0.12 has 266 motif groups, 266 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.11, 0 groups are only in release 0.12.

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
1IL_97217.42351-3 bulged nucleotides, same chain
2IL_47174.5203cWW AG or water inserted cWW Y-Y.
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.331Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_65553.422Kink-turn
12IL_32390.22116S h19 IL and 23S H41 IL
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_06429.216cWW-bulge-cWW
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
18IL_31555.315Tandem sheared with inserted, unpaired purine.
19IL_94430.31516S h32-h33-h34 3WJ
20IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_40090.21116S h34 ILa : Part of larger motif
23IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_46648.11123S H91 IL | Single-Base Intercalation Site
25IL_27618.21123S H73 ILa : Part of larger Motif
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_58291.29Recurrent Sub-motif found in junctions
28IL_47444.39SRP Loop E-like motif
29IL_92114.39GAAA loop receptor "platform" motif
30IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_90459.28cWW AG or UU
33IL_86357.27LSU Helix 61 IL2
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_73000.27cHS-cWS
36IL_08926.1623S H91 IL
37IL_53635.26LSU Helix 32 (H32) IL
38IL_72158.26LSU Helix 62 (H62) IL
39IL_89088.1616S h19 IL and 23S H41 IL
40IL_25230.26Bacterial 5S rRNA Loop E
41IL_70237.36
42IL_97057.26
43IL_13069.26LSU 3WJ H32-H33-H35A
44IL_24022.26
45IL_54420.16
46IL_10007.16Single sheared with bulged bases
47IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
48IL_79083.25
49IL_92484.15
50IL_82188.15LSU H68 IL from H.m.
51IL_01239.15
52IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
53IL_77263.15Kink-turn from U4
54IL_90133.15
55IL_02359.25
56IL_45262.25
57IL_78732.35Double S-turn motif
58IL_22732.14tSH-inserted-tHS
59IL_28572.1416S h18 kink-turn like motif
60IL_39526.34
61IL_40387.44LSU Helix 89 (H89) IL2
62IL_31066.24SSU Helix 44 (h44) extension
63IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
64IL_98556.34
65IL_10005.14
66IL_21333.14tSH-tHW-bulge
67IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
68IL_38807.24
69IL_98591.24
70IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
71IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
72IL_95150.33
73IL_16166.23
74IL_23262.33
75IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
76IL_09348.33cWW-L-cWW-cWW
77IL_16252.2323S H91 IL
78IL_30840.13
79IL_34156.43cWW AG or UU
80IL_53774.13Single sheared with bulged bases
81IL_62499.43
82IL_98421.23SSU Helix 12 (h12) IL
83IL_34363.13Kink-turn from 23S H42
84IL_52173.13
85IL_58586.23
86IL_79955.23SSU Helix (23) h23 IL1
87IL_34628.23Kink-turn
88IL_43946.13
89IL_82563.13Thi-box riboswitch T-loop
90IL_91547.13tHS tHH bulge with S-turn
91IL_36254.13
92IL_80494.23LSU H58 IL2 H.m.
93IL_37053.13Kink-turn from 23S H58
94IL_71565.13
95IL_75447.13
96IL_15840.22Triple Sheared with unpaired, inserted A
97IL_25174.12
98IL_37197.12
99IL_45794.12
100IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
101IL_76095.32Motif from Hairpin Ribozyme
102IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
103IL_12211.12
104IL_28942.12
105IL_33965.12tHS tHH bulge with S-turn
106IL_55287.12
107IL_81441.12
108IL_23414.12
109IL_37406.12
110IL_46435.12
111IL_50521.12
112IL_69901.12
113IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
114IL_89231.12LSU H77
115IL_00998.12
116IL_09882.12
117IL_16330.12
118IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
119IL_77076.12
120IL_91132.12
121IL_01054.12
122IL_16377.12
123IL_58811.12
124IL_70280.12Double sheared with wobble cWW.
125IL_74876.12
126IL_80093.12
127IL_87548.12
128IL_90057.12
129IL_98566.12
130IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
131IL_40892.12
132IL_52940.12
133IL_65137.12Kink-turn like motif in Group I Intron
134IL_21495.12
135IL_31707.12Vitamin B12 aptamer
136IL_94744.12Sarcin-ricin motif with extra cWW GA pair
137IL_07300.12
138IL_11751.12
139IL_41397.22LSU Helix 96 (H96) IL2
140IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
141IL_82831.22Kink-turn from 16S H23
142IL_97833.12
143IL_06306.11
144IL_11869.11
145IL_18755.11
146IL_47968.11
147IL_53423.11
148IL_57977.11
149IL_61730.11
150IL_66744.11SSU Helix 21 (h21) IL2 E.coli
151IL_71942.11
152IL_81398.11
153IL_83250.1116S h40 3WJ T.th.
154IL_91044.11
155IL_92280.11
156IL_97842.11
157IL_98924.11
158IL_02835.11
159IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
160IL_20775.11tSH-inserted
161IL_25181.11
162IL_37347.11
163IL_41791.11
164IL_46306.11
165IL_61991.11
166IL_67735.11
167IL_76256.11
168IL_78809.11
169IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170IL_91078.11
171IL_97961.11
172IL_02957.11
173IL_12486.11
174IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
175IL_41864.11Part of H71 junction in 23S rRNA from T.th.
176IL_55649.11
177IL_58454.11
178IL_76486.11Sarcin-ricin motif with syn G
179IL_82113.11
180IL_83856.11
181IL_91089.11
182IL_96031.11tHS tHH bulge with S-turn
183IL_03110.11
184IL_06468.1116S h40 3WJ E.c.
185IL_12507.11
186IL_23639.11tWH-tHS-L-cWW
187IL_37715.11
188IL_40527.11Kink-turn
189IL_43316.11
190IL_53988.11
191IL_55934.11kink-turn-like
192IL_83920.11
193IL_87544.11
194IL_89794.11
195IL_03282.11
196IL_06471.11
197IL_25307.11
198IL_31241.11
199IL_37990.11
200IL_40845.11
201IL_52509.11
202IL_63952.11
203IL_77195.11
204IL_85510.11
205IL_97073.11
206IL_03741.11
207IL_06808.11Double sheared (tSH-tSH) one bulged base.
208IL_13682.11
209IL_21421.11
210IL_26868.11
211IL_54450.11
212IL_59529.11
213IL_75415.11Pseudo-knot forming internal loop
214IL_82601.11Tandem cWW water-inserted CU pairs
215IL_91904.11
216IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
217IL_05221.11
218IL_06847.11Group II Intron IL
219IL_11302.11
220IL_17603.11
221IL_26971.11
222IL_41139.11
223IL_47687.11
224IL_52958.11
225IL_54576.11
226IL_56513.11
227IL_60643.11
228IL_77296.11
229IL_80505.11
230IL_82650.11
231IL_85805.11
232IL_88367.11
233IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
234IL_02690.11
235IL_05462.11
236IL_15205.11
237IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
238IL_22579.11
239IL_25082.11
240IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
241IL_37150.11tHS tHH bulge with S-turn
242IL_39324.11
243IL_53323.11
244IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
245IL_60649.11Kink-turn
246IL_65788.11
247IL_71685.11Sarcin-like with an intercalated basepair
248IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
249IL_80652.11
250IL_86059.11
251IL_88403.11
252IL_90880.11
253IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
254IL_98688.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription