Changes in PDB files used for clustering

Release 0.7 has 192 PDB files, release 0.8 has 192 PDB files, 192 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 0.7 has 263 motif groups, release 0.8 has 263 motif groups, 263 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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_97217.2234
2IL_47174.220016S h34 ILa : Part of larger motif
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_87904.231Triple sheared
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_65553.221Kink-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_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_31555.21516S decoding site
20IL_94430.21416S h32-h33-h34 3WJ
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_92114.29GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
29IL_47444.29SRP 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_97057.26
37IL_72158.26LSU Helix 62 (H62) IL
38IL_70237.36
39IL_53635.26LSU Helix 32 (H32) IL
40IL_13069.26LSU 3WJ H32-H33-H35A
41IL_24022.26
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_08926.1623S H91 IL
47IL_77263.15Kink-turn from U4
48IL_79083.25
49IL_80179.25
50IL_01239.15
51IL_92484.15
52IL_82188.15LSU H68 IL from H.m.
53IL_07911.15
54IL_78732.35Double S-turn motif
55IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
56IL_02359.25
57IL_45262.25
58IL_40387.25
59IL_28572.1416S h18 kink-turn like motif
60IL_31066.24SSU Helix 44 (h44) extension
61IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
62IL_98591.24
63IL_64184.24
64IL_22732.14tSH-inserted-tHS
65IL_39526.24
66IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
67IL_21333.14tSH-tHW-bulge
68IL_98556.14
69IL_38807.24
70IL_34363.13Kink-turn from 23S H42
71IL_23262.33
72IL_52173.13
73IL_75447.13
74IL_45808.13
75IL_98421.13
76IL_58586.23
77IL_82563.13Thi-box riboswitch T-loop
78IL_16252.2323S H91 IL
79IL_15840.13
80IL_71565.13
81IL_79955.23SSU Helix (23) h23 IL1
82IL_95150.23
83IL_80494.23LSU H58 IL2 H.m.
84IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
85IL_30840.13
86IL_37053.13Kink-turn from 23S H58
87IL_34628.23Kink-turn
88IL_62499.23
89IL_34156.23cWW AG or UU
90IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
91IL_43946.13
92IL_09348.23
93IL_53774.13Single sheared with bulged bases
94IL_76095.32Motif from Hairpin Ribozyme
95IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
96IL_70280.12Double sheared with wobble cWW.
97IL_31707.12Vitamin B12 aptamer
98IL_98566.12
99IL_87173.12
100IL_25174.12
101IL_81441.12
102IL_92459.12
103IL_94744.12Sarcin-ricin motif with extra cWW GA pair
104IL_55287.12
105IL_37197.12
106IL_99575.12
107IL_48285.12Leadzyme Motif
108IL_80093.12
109IL_82831.22Kink-turn from 16S H23
110IL_00998.12
111IL_45794.12
112IL_50521.12
113IL_09882.12
114IL_12269.12
115IL_46435.12
116IL_23414.12
117IL_43933.12
118IL_91026.12
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_21495.12
126IL_28942.12
127IL_16330.12
128IL_40892.12
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_78674.12tHS tHH bulge with S-turn
131IL_41397.22LSU Helix 96 (H96) IL2
132IL_74876.12
133IL_14023.12
134IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
135IL_97833.12
136IL_16166.12
137IL_74291.12
138IL_01054.12
139IL_37406.12
140IL_12068.12
141IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
142IL_40845.11
143IL_88865.11
144IL_76263.11
145IL_25307.11
146IL_26868.11
147IL_55649.11
148IL_54450.11
149IL_31241.11
150IL_26241.11
151IL_71942.11
152IL_91078.11
153IL_56779.11
154IL_53323.11
155IL_59529.11
156IL_02957.11
157IL_18755.11
158IL_40527.11Kink-turn
159IL_92280.11
160IL_91379.11
161IL_11302.11
162IL_89794.11
163IL_07675.11tHS tHH bulge with S-turn
164IL_25739.11M-Box Riboswitch
165IL_37715.11
166IL_22579.11
167IL_41849.11
168IL_75328.11
169IL_95939.11
170IL_25082.11
171IL_98924.11
172IL_25181.11
173IL_82601.11Tandem cWW water-inserted CU pairs
174IL_41139.11
175IL_02835.11
176IL_68827.11Reverse Kink-Turn
177IL_22858.11
178IL_66744.11SSU Helix 21 (h21) IL2 E.coli
179IL_53988.11
180IL_20775.11tSH-inserted
181IL_61730.11
182IL_53423.11
183IL_24143.11Yeast 18S
184IL_71685.11Sarcin-like with an intercalated basepair
185IL_90880.11
186IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
187IL_96260.11
188IL_85805.11
189IL_03110.11
190IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
191IL_05462.11
192IL_06808.11Double sheared (tSH-tSH) one bulged base.
193IL_65788.11
194IL_55934.11kink-turn-like
195IL_27243.11
196IL_78809.11
197IL_13682.11
198IL_67735.11
199IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
200IL_23639.11tWH-tHS-L-cWW
201IL_17603.11
202IL_15205.11
203IL_91089.11
204IL_83250.1116S h40 3WJ T.th.
205IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
206IL_43316.11
207IL_83920.11
208IL_88403.11
209IL_80652.11
210IL_32080.11
211IL_61723.11
212IL_54576.11
213IL_76486.11Sarcin-ricin motif with syn G
214IL_37990.11
215IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
216IL_47457.11
217IL_23448.11
218IL_57977.11
219IL_39324.11
220IL_41791.11
221IL_86059.11
222IL_12507.11
223IL_06468.1116S h40 3WJ E.c.
224IL_52958.11
225IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
226IL_97073.11
227IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
228IL_29949.11
229IL_75415.11Pseudo-knot forming internal loop
230IL_06306.11
231IL_97842.11
232IL_56513.11
233IL_30390.11
234IL_60643.11
235IL_63952.11
236IL_52752.11
237IL_13942.11
238IL_80505.11
239IL_47687.11
240IL_62352.11
241IL_02690.11
242IL_11869.11
243IL_41009.11
244IL_81398.11
245IL_37347.11
246IL_46306.11
247IL_91904.11
248IL_21421.11
249IL_85510.11
250IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
251IL_82650.11
252IL_31006.11tSH-tHW-L-bif-cWW
253IL_52509.11
254IL_12486.11
255IL_12233.11
256IL_77014.11
257IL_03741.11
258IL_82113.11
259IL_05221.11
260IL_26971.11
261IL_07375.11
262IL_58454.11
263IL_88367.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription