Project name: TUBB6 [mutate: FI385A]

Status: done

Started: 2025-03-31 08:11:26
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 FI385A
Energy difference between WT (input) and mutated protein (by FoldX) 4.76719 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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                                                       (00:08:53)
[INFO]       CABS:     Running CABS flex simulation                                                (00:09:09)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:56:53)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:56:57)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:57:01)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:57:05)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:57:09)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:57:12)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:57:16)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:57:20)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:57:24)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:57:28)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:57:31)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:57:35)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:57:39)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:57:50)
[INFO]       Main:     Simulation completed successfully.                                          (01:57:54)
Show buried residues

Minimal score value
-3.9744
Maximal score value
1.8924
Average score
-0.614
Total score value
-273.8608

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 0.5636
2 R A -0.1603
3 E A 0.0000
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 -1.3983
12 C A -0.5335
13 G A 0.0000
14 N A 0.0000
15 Q A -0.6716
16 I A 0.0000
17 G A 0.0000
18 T A 0.0000
19 K A -0.7096
20 F A 0.0000
21 W A 0.0000
22 E A -0.9729
23 V A 0.0000
24 I A 0.0000
25 S A 0.0000
26 D A -1.5740
27 E A 0.0000
28 H A 0.0000
29 G A -0.7401
30 I A 0.0000
31 D A -1.7572
32 P A -1.1363
33 A A -0.6124
34 G A -1.1987
35 G A -1.2554
36 Y A 0.0000
37 V A -0.8416
38 G A -0.6370
39 D A -0.6172
40 S A -0.1786
41 A A 0.4568
42 L A 0.9272
43 Q A 0.0000
44 L A 0.1800
45 E A -0.6836
46 R A -0.6347
47 I A 0.0000
48 N A -1.0454
49 V A 0.0000
50 Y A 0.0000
51 Y A 0.0000
52 N A -1.7802
53 E A -2.5494
54 S A -1.6915
55 S A -1.3075
56 S A -1.0067
57 Q A -1.4335
58 K A -2.2109
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 -1.2244
70 P A -0.6784
71 G A -1.4109
72 T A 0.0000
73 M A -1.1155
74 D A -2.1663
75 S A -1.9997
76 V A 0.0000
77 R A -2.5681
78 S A -1.6989
79 G A -1.5299
80 P A -1.0850
81 F A 0.0000
82 G A 0.0000
83 Q A -0.8012
84 L A -0.0313
85 F A 0.6922
86 R A 0.0000
87 P A -0.6425
88 D A -1.5750
89 N A 0.0000
90 F A 1.0407
91 I A 1.0729
92 F A 1.2393
93 G A -0.3268
94 Q A -1.2699
95 T A -1.1413
96 G A -1.0067
97 A A -0.9998
98 G A -0.7359
99 N A 0.0000
100 N A -0.5415
101 W A 0.0000
102 A A 0.0000
103 K A -1.0120
104 G A 0.0000
105 H A -0.2753
106 Y A -0.4110
107 T A -0.7619
108 E A -1.2463
109 G A 0.0000
110 A A -1.2253
111 E A -2.3160
112 L A 0.0000
113 V A -1.5442
114 D A -2.6348
115 A A -1.2080
116 V A 0.0000
117 L A -1.9370
118 D A -2.8673
119 V A 0.0000
120 V A 0.0000
121 R A -3.1244
122 K A -2.5869
123 E A 0.0000
124 C A -1.9457
125 E A -2.6026
126 H A -1.7471
127 C A -1.2196
128 D A -0.9432
129 C A -0.0799
130 L A -0.5150
131 Q A -1.0231
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 -0.6082
141 G A -0.9380
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 -0.1302
151 L A 0.0000
152 I A 0.0000
153 S A -1.7502
154 K A -2.3197
155 I A 0.0000
156 R A -2.8576
157 E A -3.2602
158 E A -2.9456
159 F A -2.2415
160 P A -1.6756
161 D A -2.3528
162 R A -2.4455
163 I A 0.0000
164 M A 0.0000
165 N A 0.0000
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 0.0000
172 S A -1.1277
173 P A 0.0000
174 K A -0.9853
175 V A 0.6836
176 S A -0.4741
177 D A -1.4997
178 T A -0.4919
179 V A -0.4364
180 V A -0.0229
181 E A 0.0000
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 0.0000
191 Q A -0.7334
192 L A 0.0000
193 V A -0.8545
194 E A -1.8675
195 N A 0.0000
196 T A -1.0428
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 -1.3856
205 E A -2.3686
206 A A 0.0000
207 L A 0.0000
208 Y A -0.3402
209 D A -0.8973
210 I A 0.0000
211 C A 0.0000
212 F A 0.6034
213 R A -0.8782
214 T A 0.0000
215 L A 0.7924
216 K A -0.1720
217 L A 1.2884
218 T A 0.6112
219 T A 0.2155
220 P A 0.1135
221 T A 0.1121
222 Y A 0.3543
223 G A -0.3346
224 D A -0.6423
225 L A 0.0000
226 N A 0.0000
227 H A -0.7972
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 0.0000
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 0.0000
244 G A -1.3519
245 Q A -1.6748
246 L A 0.0000
247 N A -1.2930
248 A A 0.0000
249 D A -1.4422
250 L A 0.0000
251 R A -1.8489
252 K A -1.8064
253 L A 0.0000
254 A A -0.1491
255 V A 1.0812
256 N A -0.0963
257 M A 0.0000
258 V A 0.8913
259 P A 1.3202
260 F A 1.8924
261 P A 0.0000
262 R A 0.0544
263 L A 0.0000
264 H A -0.0126
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 0.0000
276 R A -2.2979
277 G A -1.4865
278 S A -1.0747
279 Q A 0.0000
280 Q A -1.3631
281 Y A -0.7211
282 R A -1.3696
283 A A -0.2936
284 L A 0.6808
285 T A 0.1148
286 V A 0.0000
287 P A -0.7951
288 E A -0.8424
289 L A 0.0000
290 T A 0.0000
291 Q A -1.8615
292 Q A 0.0000
293 M A 0.0000
294 F A -1.1394
295 D A -1.9937
296 A A -1.8874
297 R A -2.5412
298 N A -1.7078
299 M A 0.0000
300 M A 0.0000
301 A A 0.0000
302 A A -1.2116
303 C A -1.3136
304 D A -1.7938
305 P A 0.0000
306 R A -2.5746
307 H A -2.3506
308 G A 0.0000
309 R A -1.9324
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 -0.8222
320 P A -0.2456
321 M A -0.0142
322 S A -0.3836
323 M A -0.3982
324 K A -2.3663
325 E A -2.4012
326 V A 0.0000
327 D A -1.6750
328 E A -2.3512
329 Q A 0.0000
330 M A 0.0000
331 L A 0.3233
332 A A -0.5730
333 I A 0.0000
334 Q A -0.9237
335 S A -0.9106
336 K A -1.9774
337 N A -1.2727
338 S A -1.2817
339 S A -1.0466
340 Y A -1.2011
341 F A 0.0000
342 V A 0.0000
343 E A -1.7596
344 W A 0.0000
345 I A 0.5059
346 P A 0.2546
347 N A 0.0552
348 N A -0.4270
349 V A 0.0952
350 K A -0.2124
351 V A 0.6868
352 A A 0.0000
353 V A 0.1868
354 C A 0.0000
355 D A -0.9143
356 I A 0.0000
357 P A -0.7634
358 P A -1.1134
359 R A -1.3574
360 G A -1.3569
361 L A 0.0000
362 K A -1.8837
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 -1.5943
377 L A 0.0000
378 F A 0.0000
379 K A -2.5436
380 R A -2.1652
381 I A 0.0000
382 S A -1.8759
383 E A -2.0833
384 Q A -1.0791
385 I A 0.0000 mutated: FI385A
386 S A -1.2445
387 A A -1.3428
388 M A 0.0000
389 F A -1.1076
390 R A -2.6983
391 R A -3.2345
392 K A -2.7654
393 A A -1.3421
394 F A -0.7892
395 L A -1.0466
396 H A -1.0821
397 W A 0.2607
398 F A 0.0000
399 T A -0.9695
400 G A -1.1501
401 E A -1.4753
402 G A 0.0000
403 M A 0.0000
404 D A -1.3054
405 E A -0.9900
406 M A -0.1598
407 E A -0.9092
408 F A 0.0000
409 T A -0.7286
410 E A -1.5332
411 A A 0.0000
412 E A -1.4886
413 S A -1.7004
414 N A -1.6076
415 M A 0.0000
416 N A -2.3250
417 D A -1.8587
418 L A 0.0000
419 V A -1.4331
420 S A -1.3410
421 E A 0.0000
422 Y A 0.0000
423 Q A -1.8735
424 Q A -1.6991
425 Y A 0.0000
426 Q A -1.8593
427 D A -2.2680
428 A A 0.0000
429 T A -1.5107
430 A A -1.0532
431 N A -2.1957
432 D A -2.9626
433 G A 0.0000
434 E A -3.1466
435 E A -3.9744
436 A A 0.0000
437 F A -2.0407
438 E A -3.2607
439 D A -3.2284
440 E A 0.0000
441 E A -2.7362
442 E A -3.5138
443 E A -2.4362
444 I A -0.6706
445 D A -1.9809
446 G A -1.9807
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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, -0.614 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_9 -0.614 View CSV PDB
model_1 -0.6966 View CSV PDB
model_8 -0.7052 View CSV PDB
model_4 -0.7061 View CSV PDB
model_5 -0.707 View CSV PDB
model_10 -0.7077 View CSV PDB
CABS_average -0.7199 View CSV PDB
model_0 -0.7267 View CSV PDB
model_2 -0.7299 View CSV PDB
model_6 -0.7305 View CSV PDB
model_7 -0.7484 View CSV PDB
model_3 -0.7521 View CSV PDB
input -0.797 View CSV PDB
model_11 -0.8139 View CSV PDB