Project name: MJ_TUB_42 [mutate: IT42A]

Status: done

Started: 2025-10-27 01:11:22
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 IT42A
Energy difference between WT (input) and mutated protein (by FoldX) 0.189768 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)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       FoldX:    Building mutant model                                                       (00:04:11)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:21)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:37:55)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:37:58)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:38:02)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:38:05)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:38:09)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:38:13)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:38:16)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:38:20)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:38:23)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:38:26)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:38:29)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:38:33)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:38:36)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:38:47)
[INFO]       Main:     Simulation completed successfully.                                          (01:38:50)
Show buried residues

Minimal score value
-4.3311
Maximal score value
1.662
Average score
-0.6943
Total score value
-311.0526

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 0.4919
2 R A -0.2601
3 E A 0.0000
4 C A 0.0000
5 I A 0.0000
6 S A 0.0000
7 V A 0.0000
8 H A 0.0000
9 V A 0.0000
10 G A 0.0000
11 Q A -0.7700
12 A A -0.3551
13 G A 0.0000
14 V A 0.0000
15 Q A -0.7418
16 M A 0.0000
17 G A 0.0000
18 N A -0.5164
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.4639
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 0.4484
27 E A 0.0758
28 H A -0.5841
29 G A -0.8946
30 I A -1.0979
31 Q A -1.9785
32 P A -2.4537
33 D A -3.0359
34 G A -2.5362
35 Q A -2.2365
36 M A 0.0000
37 P A -1.7151
38 S A -1.9032
39 D A -2.8229
40 K A -2.7428
41 T A -1.5146
42 T A -1.1702 mutated: IT42A
43 G A -0.9292
44 G A -0.8238
45 G A -0.4365
46 D A 0.0000
47 D A -1.1187
48 S A 0.0000
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 0.0000
55 E A -1.1811
56 T A -0.8883
57 G A -0.8787
58 A A -0.8034
59 G A -1.3048
60 K A -1.4517
61 H A 0.0000
62 V A -0.6155
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 -1.9966
72 P A 0.0000
73 T A -1.6053
74 V A -1.7190
75 I A 0.0000
76 D A -3.2032
77 E A -3.6377
78 I A 0.0000
79 R A -3.9848
80 N A -3.6047
81 G A -2.5415
82 P A -1.6825
83 Y A 0.0000
84 R A -3.0731
85 Q A -2.1018
86 L A 0.0000
87 F A 0.0000
88 H A -0.7550
89 P A -0.8816
90 E A -1.3436
91 Q A 0.0000
92 L A -0.3788
93 I A 0.0000
94 T A -0.7846
95 G A -1.7267
96 K A -2.9279
97 E A -2.7411
98 D A -2.8543
99 A A -1.5855
100 A A -1.5176
101 N A -1.0661
102 N A 0.0000
103 Y A 0.0000
104 A A 0.0000
105 R A -0.7279
106 G A 0.0000
107 H A -0.0470
108 Y A -0.0304
109 T A -0.6987
110 I A -0.9151
111 G A 0.0000
112 K A -2.1222
113 E A -2.5516
114 I A 0.0000
115 I A 0.0000
116 D A -2.0156
117 P A -1.8547
118 V A 0.0000
119 L A -1.3032
120 D A -2.4646
121 R A 0.0000
122 I A 0.0000
123 R A -3.3046
124 K A -3.0123
125 L A 0.0000
126 S A -2.1832
127 D A -2.7468
128 Q A -1.7189
129 C A -0.7770
130 T A -0.4662
131 G A -0.0242
132 L A -0.4109
133 Q A -0.7647
134 G A 0.0000
135 F A 0.0000
136 L A 0.1179
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 -0.2793
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 -0.3200
153 L A 0.0000
154 M A 0.0000
155 E A -1.2369
156 R A 0.0000
157 L A 0.0000
158 S A -0.6707
159 V A 0.7067
160 D A -0.7847
161 Y A 0.0000
162 G A -1.2126
163 K A -2.1685
164 K A -1.8514
165 S A 0.0000
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 0.0270
176 Q A 0.5047
177 V A 1.6620
178 S A 0.6005
179 T A 0.3237
180 A A 0.7142
181 V A 0.5763
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 -1.1120
193 T A -0.6429
194 T A 0.0000
195 L A 0.0000
196 E A -1.8647
197 H A -1.6301
198 S A 0.0000
199 D A -1.1268
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 -0.3670
207 E A -0.8337
208 A A 0.0000
209 I A 0.0000
210 Y A 0.0337
211 D A -1.0359
212 I A 0.0000
213 C A 0.0000
214 R A -1.1815
215 R A -1.2930
216 N A 0.0000
217 L A 0.3278
218 D A 0.0000
219 I A 0.4657
220 E A -1.5995
221 R A -1.9130
222 P A -0.8903
223 T A 0.0000
224 Y A 0.3511
225 T A -0.2695
226 N A 0.0000
227 L A 0.0000
228 N A 0.0000
229 R A -0.3981
230 L A 0.0000
231 I A 0.0000
232 S A 0.0000
233 Q A 0.0000
234 I A 0.0000
235 V A 0.0000
236 S A 0.0000
237 S A 0.0000
238 I A 0.1944
239 T A 0.0000
240 A A 0.0000
241 S A -0.0425
242 L A 0.0000
243 R A -0.4666
244 F A -0.4850
245 D A -0.2085
246 G A -0.1648
247 A A 0.1051
248 L A -0.0036
249 N A -1.1036
250 V A -0.7318
251 D A -0.9407
252 L A 0.0000
253 T A -0.9491
254 E A -1.5199
255 F A 0.0000
256 Q A -0.8836
257 T A -0.9369
258 N A -0.9754
259 L A 0.0000
260 V A 0.0000
261 P A -0.1956
262 Y A -0.3403
263 P A -1.2732
264 R A -2.1712
265 I A 0.0000
266 H A -1.0361
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 -1.1389
279 E A -1.8410
280 K A -1.8166
281 A A -1.4507
282 Y A 0.0000
283 H A -2.0943
284 E A -2.5727
285 Q A -1.8274
286 L A 0.0000
287 S A -1.1612
288 V A 0.0000
289 A A -0.9892
290 E A -1.6135
291 I A 0.0000
292 T A 0.0000
293 N A -0.9422
294 A A 0.0000
295 C A 0.0000
296 F A -0.7502
297 E A -1.1131
298 P A -1.0230
299 A A -0.7451
300 N A 0.0000
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.3033
305 C A -1.5866
306 D A -2.4521
307 P A 0.0000
308 R A -1.7364
309 H A -2.1423
310 G A -1.2405
311 K A -0.8159
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 -1.4213
323 V A 0.2167
324 V A 0.0000
325 P A -1.1256
326 K A -2.4216
327 D A -2.0153
328 V A 0.0000
329 N A -2.1289
330 A A -1.3586
331 A A 0.0000
332 I A 0.0000
333 A A -0.7212
334 A A -0.6907
335 I A 0.0000
336 K A -1.8332
337 T A -2.0400
338 K A -3.3257
339 R A 0.0000
340 S A 0.0000
341 I A 0.0000
342 Q A 0.0000
343 F A 0.0000
344 V A 0.0000
345 D A -1.5758
346 W A 0.5009
347 C A -0.1743
348 P A -1.3715
349 T A -0.9421
350 G A -0.1773
351 F A 0.1349
352 K A -0.0644
353 V A 0.0874
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A -0.1689
358 Q A -1.3312
359 P A 0.0000
360 P A -0.6372
361 T A 0.0000
362 V A -0.2107
363 V A 0.0000
364 P A -0.7674
365 G A -0.8113
366 G A -1.0325
367 D A -1.6728
368 L A 0.0000
369 A A -0.8419
370 K A -0.5913
371 V A -0.5971
372 Q A -1.0328
373 R A -1.4469
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 -1.9963
386 E A -2.7577
387 A A 0.0000
388 W A 0.0000
389 A A -1.8287
390 R A -2.4264
391 L A 0.0000
392 D A -2.0696
393 H A -1.9814
394 K A -1.0042
395 F A 0.0000
396 D A -1.9194
397 L A -0.0890
398 M A 0.0000
399 Y A -0.7095
400 A A -0.8343
401 K A -1.8294
402 R A -2.0676
403 A A -0.5231
404 F A 0.7386
405 V A 0.0000
406 H A -0.9094
407 W A 0.5363
408 Y A 0.0000
409 V A -0.5132
410 G A -0.7865
411 E A -0.8242
412 G A -0.8461
413 M A 0.0000
414 E A -2.6643
415 E A -2.3979
416 G A -2.2304
417 E A -2.5763
418 F A 0.0000
419 S A -2.7810
420 E A -3.5499
421 A A 0.0000
422 R A -3.2003
423 E A -3.3453
424 D A -2.5249
425 M A 0.0000
426 A A -1.9496
427 A A -2.0638
428 L A 0.0000
429 E A -2.6477
430 K A -3.0679
431 D A -2.7248
432 Y A 0.0000
433 E A -3.4444
434 E A -2.7366
435 V A 0.0000
436 G A -0.8347
437 I A 0.6079
438 D A -0.0175
439 S A -1.0404
440 Y A 0.0000
441 E A -3.9447
442 D A -3.6571
443 E A 0.0000
444 D A -4.3311
445 E A -4.2704
446 G A -3.1450
447 E A -3.4970
448 E A -2.9690
Download PDB file
View in 3Dmol

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, -0.6943 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_8 -0.6943 View CSV PDB
model_9 -0.7258 View CSV PDB
model_2 -0.7261 View CSV PDB
model_1 -0.7308 View CSV PDB
model_11 -0.7334 View CSV PDB
CABS_average -0.7494 View CSV PDB
model_7 -0.7571 View CSV PDB
model_0 -0.7581 View CSV PDB
model_10 -0.7591 View CSV PDB
model_3 -0.7612 View CSV PDB
model_5 -0.7613 View CSV PDB
model_4 -0.7772 View CSV PDB
model_6 -0.8085 View CSV PDB
input -0.8487 View CSV PDB