Project name: RM26

Status: done

Started: 2020-11-21 01:05:00
Settings
Chain sequence(s) X: SMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDKMENPSTVQRGLNGEPIFDPFKGFGLTGNAPTDWNEIKGKVPVEVVQSPHSPNLYFVLLVPKVVVEYHQLDKVVKEGLEVEATDSFDPTKRLKSGSPMKDSTRESQEKLSLADGGSMSSGGATSPRKALKIEVEKQSGSSDSLLKNDFAKKPFKDESNKKLAASGEFANDKAKPLLKTDEIEKNRGMGAAVVSFYDAPYSENHTAFGLVDHIDPKKMVENYPPSWKTPKWNHHGIWDYNARNLLLQ
input PDB
Selected Chain(s) X
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with X chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:17:00)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (02:37:58)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (02:38:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (02:38:08)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (02:38:13)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (02:38:19)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (02:38:24)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (02:38:28)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (02:38:34)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (02:38:39)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (02:38:45)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (02:38:50)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (02:38:55)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (02:39:00)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (02:39:06)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (02:39:07)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (02:39:08)
[INFO]       Main:     Simulation completed successfully.                                          (02:39:13)
Show buried residues
Minimal score value
-4.1909
Maximal score value
2.0919
Average score
-0.9086
Total score value
-303.4657
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
21 S X -0.7818
22 M X -0.5789
23 S X -1.0628
24 D X -2.1394
25 S X 0.0000
26 E X 0.0000
27 V X 0.0000
28 N X -1.2532
29 Q X 0.0000
30 E X -2.5876
31 A X -2.1303
32 K X -2.4930
33 P X -1.9947
34 E X -1.4660
35 V X 0.0394
36 K X -1.0264
37 P X -0.6575
38 E X -0.7192
39 V X 0.7270
40 K X -0.9742
41 P X -1.4470
42 E X -2.4345
43 T X -2.3620
44 H X -2.7110
45 I X 0.0000
46 N X -2.0506
47 L X 0.0000
48 K X -1.1188
49 V X 0.0000
50 S X -1.1104
51 D X -1.2527
52 G X -1.3959
53 S X -1.1273
54 S X -0.7244
55 E X -0.8181
56 I X 0.4421
57 F X 1.5398
58 F X 0.6387
59 K X -0.9561
60 I X 0.0000
61 K X -1.8579
62 K X 0.0000
63 T X -1.0677
64 T X -1.1175
65 P X 0.0000
66 L X 0.0000
67 R X -0.9413
68 R X -1.4391
69 L X 0.0000
70 M X 0.0000
71 E X -1.5100
72 A X -1.1212
73 F X 0.0000
74 A X 0.0000
75 K X -3.1295
76 R X -3.0434
77 Q X -2.3948
78 G X -1.9955
79 K X -1.9782
80 E X -1.7139
81 M X -1.0583
82 D X -1.2130
83 S X 0.0000
84 L X 0.0000
85 R X -1.1028
86 F X 0.0000
87 L X -1.2707
88 Y X 0.0000
89 D X -3.0239
90 G X -2.0859
91 I X -1.1628
92 R X -1.9155
93 I X -0.6675
94 Q X -0.5871
95 A X 0.0000
96 D X -0.8369
97 Q X 0.0000
98 T X 0.0000
99 P X 0.0000
100 E X -2.5821
101 D X -2.5216
102 L X -1.6018
103 D X -2.5748
104 M X -2.8485
105 E X -4.0075
106 D X -3.6910
107 N X -3.5249
108 D X 0.0000
109 K X -2.2525
110 M X 0.0000
111 E X -1.9123
112 N X -1.0737
113 P X 0.0000
114 S X -0.7256
115 T X -0.1971
116 V X -0.0938
117 Q X -1.0061
118 R X -1.0076
119 G X -0.7312
120 L X 0.0078
121 N X -1.3964
122 G X -1.2919
123 E X -1.3381
124 P X 0.0000
125 I X 0.0000
126 F X -0.6666
127 D X -1.3346
128 P X -0.4035
129 F X 0.7231
130 K X -1.2130
131 G X 0.0000
132 F X 0.0000
133 G X 0.0000
134 L X 0.0000
135 T X -0.8317
136 G X 0.0000
137 N X -1.1817
138 A X -0.5760
139 P X -0.0088
140 T X -0.3739
141 D X -1.0833
142 W X -1.1324
143 N X -2.2913
144 E X 0.0000
145 I X -1.3423
146 K X -2.5072
147 G X -1.9582
148 K X -1.5227
149 V X 0.6110
150 P X 1.2251
151 V X 1.7872
152 E X 0.6753
153 V X 2.0919
154 V X 1.4839
155 Q X 0.0470
156 S X -0.1683
157 P X -0.8765
158 H X -1.4436
159 S X -0.8671
160 P X 0.0000
161 N X -0.8470
162 L X 0.0000
163 Y X 1.2118
164 F X 1.6445
165 V X 1.6353
166 L X 1.3143
167 L X 0.0000
168 V X 0.0000
169 P X -0.2414
170 K X -1.1274
171 V X -0.4956
172 V X -0.0745
173 V X 0.5061
174 E X -1.4244
175 Y X -0.8103
176 H X -1.6440
177 Q X -1.3849
178 L X 0.0000
179 D X -1.7337
180 K X -2.2531
181 V X 0.2259
182 V X -0.7790
183 K X -2.3644
184 E X -1.8436
185 G X -1.1411
186 L X -0.9827
187 E X -1.1245
188 V X -0.6726
189 E X -1.9036
190 A X -1.2920
191 T X -1.0537
192 D X -2.0655
193 S X -0.9282
194 F X -0.2823
195 D X -1.7741
196 P X -1.7507
197 T X -2.3537
198 K X -3.6616
199 R X -3.5233
200 L X 0.0000
201 K X -2.9117
202 S X -2.2580
203 G X -1.4760
204 S X -0.8400
205 P X 0.0000
206 M X 0.0000
207 K X 0.0000
208 D X 0.0000
209 S X 0.0000
210 T X -1.8585
211 R X -3.1208
212 E X 0.0000
213 S X -2.7821
214 Q X -3.1434
215 E X -3.3827
216 K X -3.2312
217 L X -2.3534
218 S X -1.4717
219 L X 0.0000
220 A X -0.7920
221 D X 0.0000
222 G X -1.4000
223 G X -0.9957
224 S X -0.3105
225 M X 0.6200
226 S X 0.0386
227 S X -0.8185
228 G X -0.9557
229 G X -0.8449
230 A X -0.3470
231 T X -0.5921
232 S X -1.2903
233 P X -1.7988
234 R X -3.0075
235 K X -2.6580
236 A X -0.9013
237 L X 0.1887
238 K X -1.3002
239 I X -0.7111
240 E X -2.3630
241 V X -1.8453
242 E X -2.5469
243 K X -2.4083
244 Q X -1.9987
245 S X -1.5191
246 G X -1.5915
247 S X -1.1300
248 S X -1.3060
249 D X -1.9345
250 S X -1.1171
251 L X 0.0958
252 L X -0.2194
253 K X -2.3796
254 N X -2.9179
255 D X -3.2348
256 F X 0.0000
257 A X -1.7883
258 K X -1.9460
259 K X 0.0000
260 P X -1.1211
261 F X 0.0000
262 K X 0.0000
263 D X -1.4328
264 E X -1.8320
265 S X -1.5366
266 N X -2.0990
267 K X 0.0000
268 K X -1.2622
269 L X 0.0000
270 A X 0.0000
271 A X 0.0000
272 S X 0.0000
273 G X -0.8112
274 E X -1.1609
275 F X -0.4605
276 A X -0.8129
277 N X 0.0000
278 D X -2.5259
279 K X 0.0000
280 A X -1.7949
281 K X -1.0075
282 P X 0.0668
283 L X 0.9482
284 L X 1.3326
285 K X -0.4842
286 T X 0.0000
287 D X -2.9416
288 E X -3.5480
289 I X 0.0000
290 E X -3.5740
291 K X -4.1909
292 N X -3.7315
293 R X -3.5590
294 G X -1.8555
295 M X -1.3026
296 G X 0.0000
297 A X 0.0000
298 A X 0.0000
299 V X 0.3544
300 V X 0.0000
301 S X 0.0000
302 F X 0.8451
303 Y X 0.0000
304 D X -0.5882
305 A X 0.0000
306 P X -0.2535
307 Y X 0.5729
308 S X -0.1028
309 E X -0.6346
310 N X 0.0000
311 H X -0.9658
312 T X -0.5291
313 A X 0.0000
314 F X 0.6129
315 G X 0.0000
316 L X 0.9280
317 V X 0.3505
318 D X -0.9910
319 H X -0.8303
320 I X 0.1223
321 D X 0.0000
322 P X 0.0000
323 K X -1.9071
324 K X -1.7892
325 M X -0.9999
326 V X -1.1609
327 E X -2.6049
328 N X -1.9625
329 Y X -0.7407
330 P X -0.8371
331 P X -0.5275
332 S X -0.2944
333 W X -0.2787
334 K X 0.0000
335 T X -0.6195
336 P X -1.0490
337 K X -1.4724
338 W X -1.4943
339 N X -1.6337
340 H X -2.0654
341 H X -1.6760
342 G X -0.2881
343 I X 0.5452
344 W X 0.8830
345 D X -0.5251
346 Y X 0.1936
347 N X 0.1055
348 A X 0.0663
349 R X -0.4325
350 N X -0.2152
351 L X 0.0000
352 L X -0.2259
353 L X -0.3316
354 Q X -0.7398
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.9086 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
model_1 -0.9086 View CSV PDB
model_4 -0.9104 View CSV PDB
model_2 -0.916 View CSV PDB
model_5 -0.9412 View CSV PDB
model_7 -0.9705 View CSV PDB
model_3 -0.9872 View CSV PDB
model_6 -0.9955 View CSV PDB
model_0 -0.9993 View CSV PDB
model_10 -1.0271 View CSV PDB
model_8 -1.0417 View CSV PDB
model_9 -1.0494 View CSV PDB
input -1.0758 View CSV PDB
model_11 -1.1068 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018