Project name: TUBB6 [mutate: FS394A]

Status: done

Started: 2025-03-31 08:09:36
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 FS394A
Energy difference between WT (input) and mutated protein (by FoldX) 2.35197 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                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:08:54)
[INFO]       CABS:     Running CABS flex simulation                                                (00:09:04)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:53:27)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:53:31)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:53:34)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:53:38)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:53:42)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:53:45)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:53:49)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:53:52)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:53:56)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:53:59)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:54:03)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:54:06)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:54:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:54:23)
[INFO]       Main:     Simulation completed successfully.                                          (01:54:27)
Show buried residues

Minimal score value
-3.8399
Maximal score value
2.1157
Average score
-0.6524
Total score value
-290.9904

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 0.5901
2 R A -0.3922
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 -0.9212
12 C A -0.2369
13 G A 0.0000
14 N A 0.0000
15 Q A -0.5197
16 I A 0.0000
17 G A 0.0000
18 T A 0.0000
19 K A -0.9211
20 F A 0.0000
21 W A 0.0000
22 E A -1.5178
23 V A 0.0000
24 I A 0.0000
25 S A 0.0000
26 D A -2.2130
27 E A 0.0000
28 H A 0.0000
29 G A -1.5753
30 I A 0.0000
31 D A -1.1639
32 P A -0.7079
33 A A -0.4469
34 G A -0.7121
35 G A -0.5241
36 Y A -0.0930
37 V A 0.0000
38 G A -0.8364
39 D A -1.4475
40 S A -0.7959
41 A A -0.2511
42 L A -0.2947
43 Q A 0.0000
44 L A -0.2678
45 E A -1.8824
46 R A -2.1400
47 I A -0.7859
48 N A -1.1143
49 V A 0.0000
50 Y A 0.0000
51 Y A 0.0000
52 N A -1.1231
53 E A -1.4964
54 S A -1.2805
55 S A -1.2656
56 S A 0.0000
57 Q A -1.5026
58 K A -1.1735
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 -1.6075
70 P A -1.0751
71 G A -1.4078
72 T A -1.2294
73 M A -1.2838
74 D A -2.2631
75 S A -1.7944
76 V A 0.0000
77 R A -2.7786
78 S A -1.7761
79 G A -1.5311
80 P A -0.9809
81 F A -0.6685
82 G A -1.2486
83 Q A -1.0645
84 L A 0.0000
85 F A 0.0000
86 R A -1.1374
87 P A -0.9280
88 D A -1.6905
89 N A 0.0000
90 F A 0.3949
91 I A 0.9036
92 F A 1.0763
93 G A -0.1560
94 Q A -1.5560
95 T A -1.2914
96 G A -1.3355
97 A A 0.0000
98 G A -0.9425
99 N A -0.7107
100 N A -0.5316
101 W A 0.0000
102 A A 0.0000
103 K A -0.5873
104 G A 0.0000
105 H A -0.1058
106 Y A 0.5289
107 T A -0.4084
108 E A -1.3444
109 G A 0.0000
110 A A -1.2944
111 E A -2.3913
112 L A -1.3342
113 V A 0.0000
114 D A -2.5473
115 A A -1.1641
116 V A 0.0000
117 L A -1.5981
118 D A -1.4601
119 V A 0.0000
120 V A 0.0000
121 R A -2.0235
122 K A -2.5004
123 E A 0.0000
124 C A -1.6369
125 E A -2.6317
126 H A -2.0353
127 C A -1.5398
128 D A -1.0865
129 C A -0.1953
130 L A -0.1553
131 Q A -0.4237
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 -0.2873
141 G A -0.3682
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 -0.2236
151 L A 0.0000
152 I A 0.0000
153 S A -1.4358
154 K A -2.1735
155 I A 0.0000
156 R A -2.3824
157 E A -3.2091
158 E A -2.9924
159 F A -1.7354
160 P A -1.4584
161 D A -1.6006
162 R A 0.0000
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 -0.5449
172 S A 0.0000
173 P A -0.9910
174 K A 0.0000
175 V A -0.7454
176 S A -1.0238
177 D A -1.8667
178 T A -0.7332
179 V A -0.4406
180 V A 0.0000
181 E A -0.3252
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 -1.1223
191 Q A -0.8818
192 L A 0.0000
193 V A 0.0000
194 E A -1.8189
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 -0.8167
205 E A -1.4800
206 A A 0.0000
207 L A 0.0000
208 Y A 0.7188
209 D A 0.0019
210 I A 0.0000
211 C A 0.0000
212 F A 2.1157
213 R A 0.3562
214 T A 0.0000
215 L A 1.5323
216 K A -0.3240
217 L A 0.8873
218 T A -0.0218
219 T A -0.0266
220 P A 0.4426
221 T A 0.2955
222 Y A 0.8888
223 G A 0.0466
224 D A -0.2769
225 L A 0.2666
226 N A 0.0000
227 H A -0.5769
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 -0.5827
243 P A -0.7942
244 G A -0.6852
245 Q A -0.7160
246 L A -0.1564
247 N A -0.8641
248 A A 0.0000
249 D A -1.4330
250 L A 0.0000
251 R A -1.6292
252 K A -1.4878
253 L A -0.7588
254 A A 0.0000
255 V A -0.3203
256 N A -0.3780
257 M A 0.0000
258 V A 0.0000
259 P A 0.0000
260 F A 0.0000
261 P A 0.0000
262 R A -2.3694
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 0.4048
274 T A 0.0000
275 S A -0.4049
276 R A 0.0000
277 G A -0.6541
278 S A -0.6812
279 Q A 0.0000
280 Q A -1.1285
281 Y A -0.7956
282 R A -1.7880
283 A A 0.0000
284 L A -0.6055
285 T A -0.6555
286 V A 0.0000
287 P A -1.6062
288 E A -1.5955
289 L A 0.0000
290 T A 0.0000
291 Q A -1.5684
292 Q A 0.0000
293 M A 0.0000
294 F A -0.6144
295 D A -1.4033
296 A A -1.8851
297 R A -2.3956
298 N A 0.0000
299 M A 0.0000
300 M A 0.0000
301 A A 0.0000
302 A A -1.3486
303 C A -1.7428
304 D A -3.1043
305 P A 0.0000
306 R A -2.8211
307 H A -2.4181
308 G A -2.0202
309 R A 0.0000
310 Y A 0.0000
311 L A 0.0000
312 T A 0.0000
313 V A 0.0000
314 A A 0.0431
315 T A 0.0000
316 V A 0.3050
317 F A 0.0000
318 R A 0.0000
319 G A -0.6398
320 P A -0.2449
321 M A -0.0070
322 S A -0.7796
323 M A 0.0000
324 K A -3.0897
325 E A -3.4081
326 V A 0.0000
327 D A -2.2077
328 E A -2.8451
329 Q A -2.1103
330 M A 0.0000
331 L A 0.4378
332 A A -0.2516
333 I A -0.2793
334 Q A 0.0089
335 S A -0.6411
336 K A -1.5267
337 N A -0.9397
338 S A -1.1178
339 S A -1.0490
340 Y A -1.0466
341 F A -1.0784
342 V A 0.0000
343 E A -2.0695
344 W A -1.1303
345 I A -0.4612
346 P A -0.7825
347 N A -1.4881
348 N A -0.5922
349 V A 0.0952
350 K A -0.1641
351 V A 0.2273
352 A A 0.0000
353 V A 0.1540
354 C A 0.0000
355 D A -0.8061
356 I A 0.0000
357 P A 0.0000
358 P A -1.0179
359 R A -0.9987
360 G A -0.8657
361 L A -0.9097
362 K A -1.4593
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 -1.8659
377 L A 0.0000
378 F A 0.0000
379 K A -2.2860
380 R A -2.1162
381 I A 0.0000
382 S A -1.9744
383 E A -2.3838
384 Q A 0.0000
385 F A 0.0000
386 S A -0.8667
387 A A -1.0374
388 M A 0.0000
389 F A -0.6612
390 R A -1.9633
391 R A -2.1282
392 K A -2.4971
393 A A 0.0000
394 S A -1.3102 mutated: FS394A
395 L A 0.0000
396 H A -1.0953
397 W A 0.0216
398 F A 0.0000
399 T A -0.9989
400 G A -0.9515
401 E A -1.0664
402 G A -0.6439
403 M A -0.6494
404 D A -1.4740
405 E A -1.9441
406 M A -0.8237
407 E A -1.5454
408 F A 0.0000
409 T A -1.2528
410 E A -2.2043
411 A A 0.0000
412 E A -2.0732
413 S A -2.0683
414 N A -2.0765
415 M A 0.0000
416 N A -2.7196
417 D A -2.8030
418 L A 0.0000
419 V A -1.6164
420 S A -1.6925
421 E A -1.8057
422 Y A -1.4551
423 Q A -2.1124
424 Q A -1.9174
425 Y A 0.0000
426 Q A -2.0839
427 D A -2.6224
428 A A -1.7221
429 T A -1.4591
430 A A -1.5002
431 N A -2.2664
432 D A -2.4501
433 G A 0.0000
434 E A -3.2509
435 E A -3.5688
436 A A 0.0000
437 F A -1.9340
438 E A -3.8102
439 D A -3.4879
440 E A 0.0000
441 E A -3.6113
442 E A -3.8399
443 E A -3.1152
444 I A 0.0000
445 D A -2.5779
446 G A -1.9950
Download PDB file
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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, -0.6524 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_4 -0.6524 View CSV PDB
model_8 -0.6856 View CSV PDB
model_11 -0.69 View CSV PDB
model_6 -0.7064 View CSV PDB
model_9 -0.7102 View CSV PDB
CABS_average -0.7121 View CSV PDB
model_7 -0.7185 View CSV PDB
model_5 -0.7203 View CSV PDB
model_0 -0.7223 View CSV PDB
model_1 -0.7234 View CSV PDB
model_3 -0.7296 View CSV PDB
model_2 -0.7346 View CSV PDB
model_10 -0.7514 View CSV PDB
input -0.7989 View CSV PDB