Changes in PDB files used for clustering

Release 0.11 has 197 PDB files, release 0.12 has 197 PDB files, 197 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_65553.422Kink-turn
11IL_93424.222tSH-inserted-tHW
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_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_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_40090.21116S h34 ILa : Part of larger motif
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_46648.11123S H91 IL | Single-Base Intercalation Site
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
29IL_47444.39SRP Loop E-like motif
30IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_90459.28cWW AG or UU
32IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_73000.27cHS-cWS
35IL_86357.27LSU Helix 61 IL2
36IL_53635.26LSU Helix 32 (H32) IL
37IL_72158.26LSU Helix 62 (H62) IL
38IL_70237.36
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_24022.26
41IL_54420.16
42IL_25230.26Bacterial 5S rRNA Loop E
43IL_89088.1616S h19 IL and 23S H41 IL
44IL_10007.16Single sheared with bulged bases
45IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46IL_97057.26
47IL_08926.1623S H91 IL
48IL_77263.15Kink-turn from U4
49IL_01239.15
50IL_90133.15
51IL_92484.15
52IL_79083.25
53IL_82188.15LSU H68 IL from H.m.
54IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
55IL_78732.35Double S-turn motif
56IL_02359.25
57IL_45262.25
58IL_28572.1416S h18 kink-turn like motif
59IL_31066.24SSU Helix 44 (h44) extension
60IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_10005.14
62IL_98591.24
63IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
64IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
65IL_22732.14tSH-inserted-tHS
66IL_40387.44LSU Helix 89 (H89) IL2
67IL_39526.34
68IL_21333.14tSH-tHW-bulge
69IL_98556.34
70IL_38807.24
71IL_23262.33
72IL_52173.13
73IL_36254.13
74IL_09348.33cWW-L-cWW-cWW
75IL_98421.23SSU Helix 12 (h12) IL
76IL_58586.23
77IL_75447.13
78IL_16252.2323S H91 IL
79IL_95150.33
80IL_71565.13
81IL_82563.13Thi-box riboswitch T-loop
82IL_79955.23SSU Helix (23) h23 IL1
83IL_80494.23LSU H58 IL2 H.m.
84IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
85IL_37053.13Kink-turn from 23S H58
86IL_30840.13
87IL_53774.13Single sheared with bulged bases
88IL_34628.23Kink-turn
89IL_91547.13tHS tHH bulge with S-turn
90IL_62499.43
91IL_34156.43cWW AG or UU
92IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
93IL_16166.23
94IL_34363.13Kink-turn from 23S H42
95IL_43946.13
96IL_76095.32Motif from Hairpin Ribozyme
97IL_98566.12
98IL_01054.12
99IL_15840.22Triple Sheared with unpaired, inserted A
100IL_70280.12Double sheared with wobble cWW.
101IL_94744.12Sarcin-ricin motif with extra cWW GA pair
102IL_40892.12
103IL_58811.12
104IL_31707.12Vitamin B12 aptamer
105IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
106IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
107IL_81441.12
108IL_89231.12LSU H77
109IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
110IL_80093.12
111IL_00998.12
112IL_55287.12
113IL_50521.12
114IL_09882.12
115IL_77076.12
116IL_46435.12
117IL_82831.22Kink-turn from 16S H23
118IL_28942.12
119IL_87548.12
120IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
121IL_52940.12
122IL_90057.12
123IL_12211.12
124IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
125IL_23414.12
126IL_07300.12
127IL_37197.12
128IL_11751.12
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_91132.12
131IL_21495.12
132IL_33965.12tHS tHH bulge with S-turn
133IL_74876.12
134IL_45794.12
135IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
136IL_97833.12
137IL_37406.12
138IL_41397.22LSU Helix 96 (H96) IL2
139IL_69901.12
140IL_25174.12
141IL_16377.12
142IL_16330.12
143IL_96446.12
144IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
145IL_40845.11
146IL_88865.11
147IL_76263.11
148IL_25307.11
149IL_55649.11
150IL_52509.11
151IL_22579.11
152IL_77014.11
153IL_03741.11
154IL_81398.11
155IL_37347.11
156IL_46306.11
157IL_41864.11Part of H71 junction in 23S rRNA from T.th.
158IL_91044.11
159IL_27668.11
160IL_92280.11
161IL_91379.11
162IL_26868.11
163IL_89794.11
164IL_37150.11tHS tHH bulge with S-turn
165IL_37715.11
166IL_55934.11kink-turn-like
167IL_27243.11
168IL_71942.11
169IL_91078.11
170IL_82113.11
171IL_05221.11
172IL_06471.11
173IL_56513.11
174IL_85510.11
175IL_06847.11Group II Intron IL
176IL_02835.11
177IL_68827.11Reverse Kink-Turn
178IL_96031.11tHS tHH bulge with S-turn
179IL_11302.11
180IL_53988.11
181IL_61730.11
182IL_75328.11
183IL_87544.11
184IL_25082.11
185IL_53323.11
186IL_26971.11
187IL_91904.11
188IL_21421.11
189IL_88367.11
190IL_60649.11Kink-turn
191IL_85805.11
192IL_03110.11
193IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
194IL_98688.11
195IL_66744.11SSU Helix 21 (h21) IL2 E.coli
196IL_05462.11
197IL_20775.11tSH-inserted
198IL_65788.11
199IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
200IL_78809.11
201IL_53423.11
202IL_77195.11
203IL_98924.11
204IL_59529.11
205IL_02957.11
206IL_58454.11
207IL_40527.11Kink-turn
208IL_77296.11
209IL_83250.1116S h40 3WJ T.th.
210IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
211IL_41791.11
212IL_43316.11
213IL_83920.11
214IL_06808.11Double sheared (tSH-tSH) one bulged base.
215IL_11869.11
216IL_54576.11
217IL_13682.11
218IL_67735.11
219IL_97961.11
220IL_71685.11Sarcin-like with an intercalated basepair
221IL_25181.11
222IL_47968.11
223IL_18755.11
224IL_41139.11
225IL_03282.11
226IL_57977.11
227IL_39324.11
228IL_86059.11
229IL_12507.11
230IL_88403.11
231IL_52958.11
232IL_80652.11
233IL_02690.11
234IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
235IL_23639.11tWH-tHS-L-cWW
236IL_82601.11Tandem cWW water-inserted CU pairs
237IL_91089.11
238IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
239IL_63952.11
240IL_80505.11
241IL_06468.1116S h40 3WJ E.c.
242IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
243IL_97073.11
244IL_12486.11
245IL_31241.11
246IL_75415.11Pseudo-knot forming internal loop
247IL_06306.11
248IL_76486.11Sarcin-ricin motif with syn G
249IL_37990.11
250IL_90880.11
251IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
252IL_23448.11
253IL_57285.11
254IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
255IL_82650.11
256IL_61991.11
257IL_47687.11
258IL_31006.11tSH-tHW-L-bif-cWW
259IL_54450.11
260IL_76256.11
261IL_83856.11
262IL_97842.11
263IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
264IL_17603.11
265IL_15205.11
266IL_60643.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription