Project name: TUBB6 [mutate: ED125A]

Status: done

Started: 2025-04-01 08:30:34
Chain sequence(s) A: MREIVHIQAGQCGNQIGTKFWEVISDEHGIDPAGGYVGDSALQLERINVYYNESSSQKYVPRAALVDLEPGTMDSVRSGPFGQLFRPDNFIFGQTGAGNNWAKGHYTEGAELVDAVLDVVRKECEHCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEFPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDARNMMAACDPRHGRYLTVATVFRGPMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMASTFIGNSTAIQELFKRISEQFSAMFRRKAFLHWFTGEGMDEMEFTEAESNMNDLVSEYQQYQDATANDGEEAFEDEEEEIDG
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues ED125A
Energy difference between WT (input) and mutated protein (by FoldX) 0.374857 kcal/mol
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       FoldX:    Building mutant model                                                       (00:08:58)
[INFO]       CABS:     Running CABS flex simulation                                                (00:09:09)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:53:37)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:53:40)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:53:44)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:53:48)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:53:51)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:53:55)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:53:58)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:54:02)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:54:06)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:54:09)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:54:13)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:54:17)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:54:20)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:54:31)
[INFO]       Main:     Simulation completed successfully.                                          (01:54:34)
Show buried residues

Minimal score value
-3.5264
Maximal score value
2.1558
Average score
-0.5904
Total score value
-263.3082

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 M A -0.4810
2 R A -0.5320
3 E A -0.7056
4 I A 0.0000
5 V A 0.0000
6 H A 0.0000
7 I A 0.0000
8 Q A 0.0000
9 A A 0.0000
10 G A 0.0000
11 Q A -0.5181
12 C A 0.0000
13 G A 0.0000
14 N A 0.0000
15 Q A -0.3160
16 I A 0.0000
17 G A 0.0000
18 T A 0.0000
19 K A -0.4333
20 F A 0.0000
21 W A 0.0000
22 E A -0.7727
23 V A -0.7848
24 I A 0.0000
25 S A 0.0000
26 D A -1.8328
27 E A 0.0000
28 H A 0.0000
29 G A -0.2929
30 I A 0.0811
31 D A 0.0000
32 P A -0.2097
33 A A -0.7430
34 G A -0.9126
35 G A -0.9026
36 Y A -0.5759
37 V A -0.1086
38 G A -0.8059
39 D A -0.9124
40 S A -1.2152
41 A A -0.6578
42 L A -0.5827
43 Q A -1.2036
44 L A 0.0000
45 E A -2.5152
46 R A -2.0047
47 I A 0.0000
48 N A -1.1720
49 V A 0.0000
50 Y A 0.0000
51 Y A 0.0000
52 N A 0.0000
53 E A -2.2064
54 S A -1.3705
55 S A -1.2432
56 S A -1.4149
57 Q A -1.9769
58 K A -1.8001
59 Y A 0.0000
60 V A 0.0000
61 P A 0.0000
62 R A 0.0000
63 A A 0.0000
64 A A 0.0000
65 L A 0.0000
66 V A 0.0000
67 D A 0.0000
68 L A 0.0000
69 E A -0.7716
70 P A -0.8343
71 G A -1.4782
72 T A 0.0000
73 M A 0.0000
74 D A -2.6625
75 S A -1.8615
76 V A 0.0000
77 R A -2.4188
78 S A -1.4976
79 G A -1.2392
80 P A -0.4115
81 F A -0.0503
82 G A -0.7429
83 Q A -0.3040
84 L A 0.2986
85 F A 0.1167
86 R A 0.0000
87 P A -1.2803
88 D A -2.1533
89 N A -0.6709
90 F A 0.2470
91 I A 0.0000
92 F A 1.3639
93 G A -0.2603
94 Q A -1.2711
95 T A -0.6860
96 G A -0.7347
97 A A -0.6887
98 G A -0.6248
99 N A -0.5882
100 N A 0.0000
101 W A 0.0000
102 A A 0.0000
103 K A -0.2920
104 G A 0.0000
105 H A -0.0405
106 Y A 0.4817
107 T A -0.3887
108 E A 0.0000
109 G A 0.0000
110 A A -1.1346
111 E A -2.2693
112 L A 0.0000
113 V A 0.0000
114 D A -2.6137
115 A A -1.5356
116 V A 0.0000
117 L A 0.0000
118 D A -2.2486
119 V A 0.0000
120 V A 0.0000
121 R A -2.5467
122 K A -2.8731
123 E A 0.0000
124 C A -2.1809
125 D A -3.1468 mutated: ED125A
126 H A -2.6045
127 C A -2.1148
128 D A -2.2339
129 C A -1.3809
130 L A 0.0000
131 Q A -1.0233
132 G A 0.0000
133 F A 0.0000
134 Q A 0.0000
135 L A 0.0000
136 T A 0.0000
137 H A 0.0000
138 S A 0.0000
139 L A 0.0000
140 G A 0.0000
141 G A 0.0000
142 G A 0.0000
143 T A 0.0000
144 G A 0.0000
145 S A 0.0000
146 G A 0.0000
147 M A 0.0000
148 G A 0.0000
149 T A 0.0000
150 L A 0.0780
151 L A 0.0000
152 I A 0.0000
153 S A -1.0912
154 K A -1.7995
155 I A 0.0000
156 R A -2.2628
157 E A -3.3008
158 E A -3.2998
159 F A 0.0000
160 P A -1.8429
161 D A -2.4096
162 R A 0.0000
163 I A 0.0000
164 M A -0.5559
165 N A -0.2167
166 T A 0.0000
167 F A 0.0000
168 S A 0.0000
169 V A 0.0000
170 M A 0.0000
171 P A -0.5383
172 S A 0.0000
173 P A -0.2049
174 K A 0.0000
175 V A -0.1945
176 S A -0.0873
177 D A -0.0044
178 T A 0.6427
179 V A 1.5909
180 V A 0.0000
181 E A 0.2395
182 P A 0.0000
183 Y A 0.0000
184 N A 0.0000
185 A A 0.0000
186 T A 0.0000
187 L A 0.0000
188 S A 0.0000
189 V A 0.0000
190 H A -0.7298
191 Q A -0.4020
192 L A 0.0000
193 V A 0.0000
194 E A -1.1606
195 N A 0.0000
196 T A 0.0000
197 D A 0.0000
198 E A 0.0000
199 T A 0.0000
200 Y A 0.0000
201 C A 0.0000
202 I A 0.0000
203 D A 0.0000
204 N A 0.0000
205 E A -1.1694
206 A A 0.0000
207 L A 0.0000
208 Y A 0.9632
209 D A -0.4894
210 I A 0.0000
211 C A 0.0000
212 F A 2.0466
213 R A -0.1114
214 T A 0.3589
215 L A 1.7841
216 K A 0.0000
217 L A 2.1558
218 T A 0.7932
219 T A 0.4873
220 P A 0.6564
221 T A 1.2078
222 Y A 0.8462
223 G A 0.0460
224 D A 0.0000
225 L A 0.0000
226 N A 0.0000
227 H A -0.4670
228 L A 0.0000
229 V A 0.0000
230 S A 0.0000
231 A A 0.0000
232 T A 0.0000
233 M A 0.0000
234 S A 0.0000
235 G A 0.0000
236 V A 0.2494
237 T A 0.0000
238 T A 0.0000
239 S A 0.0000
240 L A 0.0000
241 R A 0.0000
242 F A 0.0000
243 P A -1.0104
244 G A -1.2533
245 Q A -1.7936
246 L A 0.0000
247 N A -1.7151
248 A A -1.1681
249 D A 0.0000
250 L A 0.0000
251 R A -0.9475
252 K A -0.9558
253 L A 0.0000
254 A A 0.0000
255 V A 0.7015
256 N A -0.5467
257 M A 0.0000
258 V A 0.0000
259 P A 0.2938
260 F A 0.0000
261 P A 0.0000
262 R A -0.7376
263 L A 0.0000
264 H A 0.0000
265 F A 0.0000
266 F A 0.0000
267 M A 0.0000
268 P A 0.0000
269 G A 0.0000
270 F A 0.0000
271 A A 0.0000
272 P A 0.0000
273 L A 0.0000
274 T A 0.0000
275 S A -1.0698
276 R A -1.8416
277 G A -1.2747
278 S A -1.1018
279 Q A -1.4921
280 Q A -1.6217
281 Y A -0.8844
282 R A -0.9221
283 A A -0.1021
284 L A -0.1162
285 T A -0.2557
286 V A -0.4211
287 P A -0.8731
288 E A -1.0769
289 L A 0.0000
290 T A 0.0000
291 Q A -1.6561
292 Q A 0.0000
293 M A 0.0000
294 F A -1.4485
295 D A -2.2825
296 A A -2.4168
297 R A -2.7348
298 N A 0.0000
299 M A 0.0000
300 M A 0.0000
301 A A 0.0000
302 A A -1.5521
303 C A 0.0000
304 D A -3.3545
305 P A 0.0000
306 R A -3.0928
307 H A -2.7523
308 G A 0.0000
309 R A -1.9178
310 Y A 0.0000
311 L A 0.0000
312 T A 0.0000
313 V A 0.0000
314 A A 0.0000
315 T A 0.0000
316 V A 0.0000
317 F A 0.0000
318 R A 0.0000
319 G A 0.0000
320 P A -0.0461
321 M A -0.0988
322 S A -0.3895
323 M A -0.4442
324 K A -2.4885
325 E A -2.8465
326 V A 0.0000
327 D A -1.9018
328 E A -2.4766
329 Q A -1.5198
330 M A 0.0000
331 L A -0.4833
332 A A -0.5853
333 I A -0.8040
334 Q A -1.1402
335 S A -1.1164
336 K A -1.7778
337 N A -1.3669
338 S A -1.2953
339 S A -1.4434
340 Y A 0.0000
341 F A 0.0000
342 V A 0.0000
343 E A -1.7821
344 W A -0.7332
345 I A 0.0000
346 P A -1.3181
347 N A -1.4827
348 N A -1.0341
349 V A -0.2618
350 K A -0.2476
351 V A 0.3549
352 A A 0.2417
353 V A 0.5069
354 C A 0.0000
355 D A -0.4971
356 I A 0.0000
357 P A 0.0000
358 P A -0.3127
359 R A -0.7718
360 G A -0.2354
361 L A 0.6892
362 K A -0.3136
363 M A 0.0000
364 A A 0.0000
365 S A 0.0000
366 T A 0.0000
367 F A 0.0000
368 I A 0.0000
369 G A 0.0000
370 N A 0.0000
371 S A 0.0000
372 T A 0.0000
373 A A 0.0000
374 I A 0.0000
375 Q A 0.0000
376 E A -2.8355
377 L A -1.6916
378 F A 0.0000
379 K A -2.3551
380 R A -2.4670
381 I A 0.0000
382 S A -1.9527
383 E A -2.5774
384 Q A -1.1559
385 F A 0.0000
386 S A -1.3704
387 A A -1.3643
388 M A 0.0000
389 F A -0.7901
390 R A -2.4814
391 R A -3.0531
392 K A -2.7294
393 A A -1.3278
394 F A -0.3701
395 L A -1.1540
396 H A -1.5592
397 W A -0.4336
398 F A 0.0000
399 T A -1.3288
400 G A -1.2809
401 E A -0.9492
402 G A -0.9214
403 M A 0.0000
404 D A -1.8523
405 E A -2.1697
406 M A -0.5904
407 E A -1.2148
408 F A 0.0000
409 T A -0.9094
410 E A -1.3878
411 A A 0.0000
412 E A -1.7041
413 S A -1.5592
414 N A -1.5614
415 M A 0.0000
416 N A -2.1678
417 D A -1.7677
418 L A 0.0000
419 V A 0.0000
420 S A -1.5267
421 E A -1.5483
422 Y A 0.0000
423 Q A -2.5601
424 Q A -2.5549
425 Y A 0.0000
426 Q A -2.4114
427 D A -2.9787
428 A A 0.0000
429 T A -1.6069
430 A A -1.7146
431 N A -2.3735
432 D A -2.7158
433 G A 0.0000
434 E A -2.4123
435 E A -3.1382
436 A A 0.0000
437 F A -1.7962
438 E A -3.5264
439 D A -2.9557
440 E A 0.0000
441 E A -3.1999
442 E A -2.9768
443 E A -1.4979
444 I A 0.2444
445 D A -0.8985
446 G A -0.6452
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D 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 A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.5904 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 A4D Score
model_1 -0.5904 View CSV PDB
model_0 -0.6196 View CSV PDB
model_2 -0.6391 View CSV PDB
model_4 -0.641 View CSV PDB
model_10 -0.6564 View CSV PDB
model_5 -0.6708 View CSV PDB
model_8 -0.6713 View CSV PDB
CABS_average -0.6795 View CSV PDB
model_11 -0.7194 View CSV PDB
model_6 -0.7212 View CSV PDB
model_3 -0.7247 View CSV PDB
model_7 -0.7441 View CSV PDB
model_9 -0.7559 View CSV PDB
input -0.7993 View CSV PDB