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_85647.216Sarcin-ricin parent motif with 15 Nts
17IL_06429.216cWW-bulge-cWW
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_94430.31516S h32-h33-h34 3WJ
20IL_31555.315Tandem sheared with inserted, unpaired purine.
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_46648.11123S H91 IL | Single-Base Intercalation Site
23IL_40090.21116S h34 ILa : Part of larger motif
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.39SRP Loop E-like motif
28IL_92114.39GAAA loop receptor "platform" motif
29IL_58291.29Recurrent Sub-motif found in junctions
30IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_90459.28cWW AG or UU
32IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
33IL_73000.27cHS-cWS
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_86357.27LSU Helix 61 IL2
36IL_13069.26LSU 3WJ H32-H33-H35A
37IL_70237.36
38IL_24022.26
39IL_54420.16
40IL_25230.26Bacterial 5S rRNA Loop E
41IL_89088.1616S h19 IL and 23S H41 IL
42IL_10007.16Single sheared with bulged bases
43IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_97057.26
45IL_08926.1623S H91 IL
46IL_53635.26LSU Helix 32 (H32) IL
47IL_72158.26LSU Helix 62 (H62) IL
48IL_01239.15
49IL_92484.15
50IL_02359.25
51IL_82188.15LSU H68 IL from H.m.
52IL_78732.35Double S-turn motif
53IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
54IL_45262.25
55IL_79083.25
56IL_77263.15Kink-turn from U4
57IL_90133.15
58IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_10005.14
60IL_98591.24
61IL_40387.44LSU Helix 89 (H89) IL2
62IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
63IL_22732.14tSH-inserted-tHS
64IL_39526.34
65IL_98556.34
66IL_38807.24
67IL_21333.14tSH-tHW-bulge
68IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
69IL_28572.1416S h18 kink-turn like motif
70IL_31066.24SSU Helix 44 (h44) extension
71IL_52173.13
72IL_58586.23
73IL_82563.13Thi-box riboswitch T-loop
74IL_34628.23Kink-turn
75IL_98421.23SSU Helix 12 (h12) IL
76IL_71565.13
77IL_30840.13
78IL_53774.13Single sheared with bulged bases
79IL_95150.33
80IL_80494.23LSU H58 IL2 H.m.
81IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
82IL_79955.23SSU Helix (23) h23 IL1
83IL_37053.13Kink-turn from 23S H58
84IL_34156.43cWW AG or UU
85IL_23262.33
86IL_62499.43
87IL_34363.13Kink-turn from 23S H42
88IL_43946.13
89IL_09348.33cWW-L-cWW-cWW
90IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
91IL_16166.23
92IL_16252.2323S H91 IL
93IL_91547.13tHS tHH bulge with S-turn
94IL_36254.13
95IL_75447.13
96IL_31707.12Vitamin B12 aptamer
97IL_28942.12
98IL_16377.12
99IL_16330.12
100IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
101IL_80093.12
102IL_82831.22Kink-turn from 16S H23
103IL_74876.12
104IL_40892.12
105IL_58811.12
106IL_89231.12LSU H77
107IL_46435.12
108IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
109IL_33965.12tHS tHH bulge with S-turn
110IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
111IL_50521.12
112IL_09882.12
113IL_77076.12
114IL_12211.12
115IL_21495.12
116IL_37406.12
117IL_41397.22LSU Helix 96 (H96) IL2
118IL_69901.12
119IL_25174.12
120IL_87548.12
121IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
122IL_52940.12
123IL_90057.12
124IL_91132.12
125IL_70280.12Double sheared with wobble cWW.
126IL_94744.12Sarcin-ricin motif with extra cWW GA pair
127IL_55287.12
128IL_11751.12
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_01054.12
131IL_15840.22Triple Sheared with unpaired, inserted A
132IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
133IL_97833.12
134IL_98566.12
135IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
136IL_81441.12
137IL_23414.12
138IL_07300.12
139IL_37197.12
140IL_76095.32Motif from Hairpin Ribozyme
141IL_00998.12
142IL_45794.12
143IL_92280.11
144IL_02835.11
145IL_68827.11Reverse Kink-Turn
146IL_98688.11
147IL_66744.11SSU Helix 21 (h21) IL2 E.coli
148IL_06808.11Double sheared (tSH-tSH) one bulged base.
149IL_11869.11
150IL_83856.11
151IL_97842.11
152IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
153IL_17603.11
154IL_15205.11
155IL_91044.11
156IL_03110.11
157IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
158IL_83920.11
159IL_52958.11
160IL_80652.11
161IL_02690.11
162IL_03741.11
163IL_81398.11
164IL_37347.11
165IL_46306.11
166IL_41864.11Part of H71 junction in 23S rRNA from T.th.
167IL_06847.11Group II Intron IL
168IL_85805.11
169IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170IL_41791.11
171IL_43316.11
172IL_88403.11
173IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
174IL_97073.11
175IL_12486.11
176IL_31241.11
177IL_76256.11
178IL_91078.11
179IL_82113.11
180IL_05221.11
181IL_06471.11
182IL_56513.11
183IL_85510.11
184IL_60649.11Kink-turn
185IL_83250.1116S h40 3WJ T.th.
186IL_57977.11
187IL_39324.11
188IL_86059.11
189IL_12507.11
190IL_06468.1116S h40 3WJ E.c.
191IL_54450.11
192IL_71942.11
193IL_87544.11
194IL_25082.11
195IL_53323.11
196IL_26971.11
197IL_91904.11
198IL_21421.11
199IL_88367.11
200IL_77296.11
201IL_80505.11
202IL_61991.11
203IL_47687.11
204IL_55649.11
205IL_52509.11
206IL_22579.11
207IL_53423.11
208IL_77195.11
209IL_98924.11
210IL_59529.11
211IL_02957.11
212IL_58454.11
213IL_40527.11Kink-turn
214IL_03282.11
215IL_63952.11
216IL_82650.11
217IL_89794.11
218IL_37150.11tHS tHH bulge with S-turn
219IL_37715.11
220IL_55934.11kink-turn-like
221IL_61730.11
222IL_13682.11
223IL_67735.11
224IL_97961.11
225IL_71685.11Sarcin-like with an intercalated basepair
226IL_25181.11
227IL_47968.11
228IL_18755.11
229IL_41139.11
230IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
231IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
232IL_76263.11
233IL_25307.11
234IL_26868.11
235IL_53988.11
236IL_78809.11
237IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
238IL_23639.11tWH-tHS-L-cWW
239IL_82601.11Tandem cWW water-inserted CU pairs
240IL_91089.11
241IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
242IL_40845.11
243IL_96031.11tHS tHH bulge with S-turn
244IL_11302.11
245IL_05462.11
246IL_20775.11tSH-inserted
247IL_65788.11
248IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
249IL_54576.11
250IL_75415.11Pseudo-knot forming internal loop
251IL_06306.11
252IL_76486.11Sarcin-ricin motif with syn G
253IL_37990.11
254IL_90880.11
255IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
256IL_60643.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription