Project name: mj_TUBA_371 [mutate: VM371A]

Status: done

Started: 2026-07-15 03:03:51
Chain sequence(s) A: MRECISVHVGQAGVQMGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFTTFFCETGAGKHVPRAVFVDLEPTVIDEIRNGPYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDPVLDRIRKLSDQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIAAIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGIDSYEDEDEGEE
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 VM371A
Energy difference between WT (input) and mutated protein (by FoldX) -0.679223 kcal/mol
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:04:58)
[INFO]       CABS:     Running CABS flex simulation                                                (00:05:04)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:11:19)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:11:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:11:24)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:11:26)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:11:28)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:11:30)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:11:33)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:11:35)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:11:37)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:11:39)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:11:41)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:11:43)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:11:46)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:11:52)
[INFO]       Main:     Simulation completed successfully.                                          (01:11:54)
Show buried residues

Minimal score value
-3.7145
Maximal score value
1.5793
Average score
-0.6671
Total score value
-298.8457

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 -0.5721
2 R A -0.6415
3 E A 0.0000
4 C A 0.0000
5 I A 0.0000
6 S A -0.0075
7 V A 0.0000
8 H A 0.0000
9 V A 0.0000
10 G A 0.0000
11 Q A -1.6328
12 A A -0.6425
13 G A 0.0000
14 V A 0.0000
15 Q A -1.0067
16 M A 0.0000
17 G A 0.0000
18 N A -1.1565
19 A A 0.0000
20 C A 0.0000
21 W A -0.2121
22 E A -0.2891
23 L A 0.0000
24 Y A 0.0000
25 C A 0.2233
26 L A 0.3798
27 E A -0.2122
28 H A 0.0711
29 G A 0.3858
30 I A 0.3400
31 Q A -1.2336
32 P A -1.3934
33 D A -2.4849
34 G A -1.7032
35 Q A 0.0000
36 M A 0.3197
37 P A -0.0806
38 S A -1.3979
39 D A -2.7058
40 K A -2.7875
41 T A -1.4934
42 I A -0.8179
43 G A -0.8085
44 G A -1.1532
45 G A -1.3308
46 D A -1.3229
47 D A -1.5943
48 S A -1.0663
49 F A 0.0000
50 T A 0.0000
51 T A 0.0000
52 F A 0.0000
53 F A 0.0000
54 C A -0.7717
55 E A -1.1961
56 T A -1.0644
57 G A -1.0776
58 A A -0.8708
59 G A -1.3813
60 K A -1.8108
61 H A 0.0000
62 V A -0.2647
63 P A 0.0000
64 R A 0.0000
65 A A 0.0000
66 V A 0.0000
67 F A 0.0000
68 V A 0.0000
69 D A 0.0000
70 L A 0.0000
71 E A -3.1873
72 P A 0.0000
73 T A -1.8279
74 V A 0.0000
75 I A 0.0000
76 D A -2.9017
77 E A -3.5079
78 I A 0.0000
79 R A -3.5031
80 N A -3.1603
81 G A -2.2078
82 P A -1.5437
83 Y A -0.9441
84 R A -2.4200
85 Q A -1.6370
86 L A -0.4452
87 F A -0.7224
88 H A -1.6267
89 P A -1.7387
90 E A -2.2318
91 Q A -1.4749
92 L A -1.0816
93 I A 0.0000
94 T A -1.3369
95 G A 0.0000
96 K A -3.5961
97 E A -3.7145
98 D A -3.2776
99 A A -1.9448
100 A A -1.0626
101 N A 0.0000
102 N A -0.4688
103 Y A 0.0000
104 A A 0.0000
105 R A -1.3327
106 G A 0.0000
107 H A -0.3983
108 Y A -0.6162
109 T A -1.0851
110 I A 0.0000
111 G A 0.0000
112 K A -2.6872
113 E A -2.7409
114 I A 0.0000
115 I A 0.0000
116 D A -2.9923
117 P A -2.1595
118 V A 0.0000
119 L A 0.0000
120 D A -2.3801
121 R A -2.3410
122 I A 0.0000
123 R A -2.5840
124 K A -2.7178
125 L A 0.0000
126 S A -1.9556
127 D A -2.9109
128 Q A -1.9724
129 C A -0.7649
130 T A -0.7105
131 G A -0.8701
132 L A -0.5113
133 Q A -0.3437
134 G A 0.0000
135 F A 0.0000
136 L A 0.0000
137 V A 0.0000
138 F A 0.0000
139 H A 0.0000
140 S A 0.0000
141 F A 0.0000
142 G A 0.0000
143 G A 0.0000
144 G A 0.0000
145 T A 0.0000
146 G A 0.0000
147 S A 0.0000
148 G A 0.0000
149 F A 0.0000
150 T A 0.0000
151 S A 0.0000
152 L A -0.3589
153 L A 0.0000
154 M A 0.0000
155 E A -0.7269
156 R A -0.5603
157 L A 0.0000
158 S A -0.4519
159 V A 0.5808
160 D A -0.4974
161 Y A -0.7223
162 G A -1.0982
163 K A -1.9346
164 K A -1.3003
165 S A -0.7176
166 K A 0.0000
167 L A 0.0000
168 E A 0.0000
169 F A 0.0000
170 S A 0.0000
171 I A 0.0000
172 Y A 0.0000
173 P A 0.0000
174 A A 0.0000
175 P A -0.3009
176 Q A -0.1373
177 V A 1.2015
178 S A 0.6018
179 T A 1.0547
180 A A 0.4795
181 V A 0.0000
182 V A 0.0000
183 E A 0.0000
184 P A 0.0000
185 Y A 0.0000
186 N A 0.0000
187 S A 0.0000
188 I A 0.0000
189 L A 0.0000
190 T A 0.0000
191 T A 0.0000
192 H A -1.3008
193 T A 0.0000
194 T A 0.0000
195 L A -1.0203
196 E A -1.8234
197 H A -0.9706
198 S A -0.9830
199 D A 0.0000
200 C A 0.0000
201 A A 0.0000
202 F A 0.0000
203 M A 0.0000
204 V A 0.0000
205 D A 0.0000
206 N A -0.6775
207 E A -1.3982
208 A A 0.0000
209 I A 0.0000
210 Y A -0.4043
211 D A -1.7814
212 I A 0.0000
213 C A 0.0000
214 R A -3.0126
215 R A -3.2093
216 N A -2.2736
217 L A 0.0000
218 D A 0.0000
219 I A -2.1883
220 E A -2.9586
221 R A -1.5603
222 P A -0.6545
223 T A -0.0526
224 Y A 1.2392
225 T A 0.1199
226 N A 0.0000
227 L A 0.0000
228 N A 0.0000
229 R A -0.0543
230 L A 0.0000
231 I A 0.0000
232 S A 0.0000
233 Q A -0.1370
234 I A 0.0000
235 V A 0.0000
236 S A 0.0000
237 S A 0.0000
238 I A 0.1431
239 T A 0.1411
240 A A 0.0000
241 S A 0.0000
242 L A 0.0000
243 R A 0.0000
244 F A -0.1493
245 D A -1.3646
246 G A -0.4207
247 A A 0.1635
248 L A 0.0394
249 N A -0.4735
250 V A 0.0000
251 D A -0.8856
252 L A 0.0000
253 T A -0.8055
254 E A -1.1510
255 F A 0.0000
256 Q A -0.6843
257 T A -0.5466
258 N A -0.5349
259 L A 0.0000
260 V A 0.0036
261 P A 0.1540
262 Y A 0.4964
263 P A -0.9252
264 R A -1.8844
265 I A 0.0000
266 H A -0.6115
267 F A 0.0000
268 P A 0.0000
269 L A 0.0000
270 A A 0.0000
271 T A 0.0000
272 Y A 0.0000
273 A A 0.0000
274 P A 0.0000
275 V A 0.0000
276 I A 0.0000
277 S A 0.0000
278 A A -1.5911
279 E A -2.8410
280 K A -2.5926
281 A A -1.1742
282 Y A -0.6653
283 H A -1.5024
284 E A -2.4789
285 Q A -1.6610
286 L A 0.0000
287 S A -1.0540
288 V A 0.0000
289 A A -1.2264
290 E A -2.3404
291 I A 0.0000
292 T A 0.0000
293 N A -1.0806
294 A A -1.2544
295 C A 0.0000
296 F A 0.0000
297 E A -1.0339
298 P A 0.0000
299 A A -0.4332
300 N A -0.6606
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.0914
305 C A -0.6291
306 D A -1.2493
307 P A -1.0090
308 R A 0.0000
309 H A -1.2682
310 G A 0.0000
311 K A 0.0000
312 Y A 0.0000
313 M A 0.0000
314 A A 0.0000
315 C A 0.0000
316 C A 0.0000
317 L A 0.0000
318 L A 0.0000
319 Y A 0.0000
320 R A 0.0000
321 G A 0.0000
322 D A -1.4626
323 V A -0.0687
324 V A 0.0000
325 P A -0.9546
326 K A -2.2835
327 D A -1.7397
328 V A 0.0000
329 N A -1.8478
330 A A -1.2335
331 A A 0.0000
332 I A -0.8251
333 A A -0.9556
334 A A -1.1878
335 I A 0.0000
336 K A -2.2964
337 T A -1.9559
338 K A -2.7330
339 R A -2.7017
340 S A -1.9261
341 I A 0.0000
342 Q A 0.0000
343 F A -0.2722
344 V A 0.0000
345 D A -1.2269
346 W A 0.0000
347 C A -0.0656
348 P A -0.3272
349 T A -0.1057
350 G A -0.0711
351 F A 0.1274
352 K A -0.2847
353 V A -0.0310
354 G A 0.0000
355 I A 0.4593
356 N A 0.0000
357 Y A -0.1556
358 Q A -1.4797
359 P A 0.0000
360 P A -1.1887
361 T A -0.5662
362 V A 0.0000
363 V A 0.1767
364 P A 0.0000
365 G A -0.4517
366 G A -0.5099
367 D A -1.4032
368 L A 0.0000
369 A A 0.0000
370 K A -1.5686
371 M A -0.9624 mutated: VM371A
372 Q A -1.0681
373 R A -0.8435
374 A A 0.0000
375 V A 0.0000
376 C A 0.0000
377 M A 0.0000
378 L A 0.0000
379 S A 0.0000
380 N A 0.0000
381 T A 0.0000
382 T A 0.0000
383 A A 0.0000
384 I A 0.0000
385 A A -1.4704
386 E A -1.4801
387 A A 0.0000
388 W A 0.0000
389 A A -1.1329
390 R A -1.5506
391 L A 0.0000
392 D A 0.0000
393 H A -1.4517
394 K A -0.8888
395 F A 0.0000
396 D A -0.9065
397 L A -0.0003
398 M A 0.0000
399 Y A 0.2673
400 A A 0.0020
401 K A -0.7283
402 R A -1.1117
403 A A 0.0351
404 F A 1.5793
405 V A 0.7176
406 H A -0.0338
407 W A 1.0512
408 Y A 0.0000
409 V A -0.3938
410 G A -0.5684
411 E A -1.7079
412 G A -1.6383
413 M A 0.0000
414 E A -3.0223
415 E A -2.8133
416 G A -2.2066
417 E A -2.2871
418 F A 0.0000
419 S A -2.1506
420 E A -2.4157
421 A A 0.0000
422 R A -2.5026
423 E A -2.8859
424 D A -2.0706
425 M A 0.0000
426 A A -1.6938
427 A A -1.8304
428 L A 0.0000
429 E A -2.5765
430 K A -3.2468
431 D A -2.6357
432 Y A 0.0000
433 E A -3.0111
434 E A -2.4127
435 V A 0.0000
436 G A -0.9997
437 I A 0.5304
438 D A -0.4027
439 S A -0.9086
440 Y A -1.5121
441 E A -3.1887
442 D A -3.0451
443 E A -2.5254
444 D A -3.1664
445 E A 0.0000
446 G A -1.7118
447 E A -2.0769
448 E A -2.4498
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, -0.6671 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 -0.6671 View CSV PDB
model_11 -0.6737 View CSV PDB
model_6 -0.7001 View CSV PDB
model_7 -0.7146 View CSV PDB
model_2 -0.7176 View CSV PDB
model_3 -0.7181 View CSV PDB
CABS_average -0.7397 View CSV PDB
model_10 -0.7456 View CSV PDB
model_5 -0.752 View CSV PDB
model_9 -0.7533 View CSV PDB
model_1 -0.7953 View CSV PDB
input -0.8059 View CSV PDB
model_0 -0.8119 View CSV PDB
model_8 -0.8274 View CSV PDB