Project name: mj_TB_wt_dynamic [mutate: AT12A]

Status: done

Started: 2025-02-28 06:38:27
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 AT12A
Energy difference between WT (input) and mutated protein (by FoldX) -0.993638 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                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:10:34)
[INFO]       CABS:     Running CABS flex simulation                                                (00:10:41)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:11:53)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:11:55)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:11:57)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:12:00)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:12:02)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:12:04)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:12:06)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:12:08)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:12:10)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:12:12)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:12:14)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:12:16)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:12:18)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:12:25)
[INFO]       Main:     Simulation completed successfully.                                          (01:12:27)
Show buried residues

Minimal score value
-3.519
Maximal score value
1.2798
Average score
-0.6241
Total score value
-279.6001

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 0.5218
2 R A -0.3311
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 -0.8394
12 T A -0.4499 mutated: AT12A
13 G A 0.0000
14 V A 0.0000
15 Q A -1.2672
16 M A 0.0000
17 G A 0.0000
18 N A -0.8635
19 A A -0.7015
20 C A 0.0000
21 W A 0.0000
22 E A -0.5236
23 L A 0.0000
24 Y A 0.0000
25 C A 0.0000
26 L A 0.4719
27 E A 0.0000
28 H A 0.0000
29 G A 0.3151
30 I A 1.0165
31 Q A -0.3528
32 P A -1.0030
33 D A -2.3834
34 G A -2.0267
35 Q A -1.0872
36 M A 0.0000
37 P A 0.0000
38 S A -0.6510
39 D A -0.8973
40 K A -0.4894
41 T A -0.3373
42 I A 0.3432
43 G A -0.4487
44 G A -0.8110
45 G A 0.0000
46 D A 0.0000
47 D A 0.0000
48 S A 0.0000
49 F A 0.0000
50 T A -0.1509
51 T A 0.0000
52 F A 0.0000
53 F A -0.2842
54 C A 0.0000
55 E A -2.1034
56 T A -1.5233
57 G A -1.1689
58 A A -1.1352
59 G A -1.2622
60 K A -1.8107
61 H A -1.6196
62 V A 0.0000
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 -1.8857
72 P A 0.0000
73 T A -1.5952
74 V A 0.0000
75 I A 0.0000
76 D A -2.7965
77 E A -3.4652
78 I A 0.0000
79 R A -3.4764
80 N A -3.2894
81 G A -2.5169
82 P A -2.3610
83 Y A -1.9774
84 R A -2.6378
85 Q A -1.9279
86 L A 0.0000
87 F A 0.0000
88 H A 0.0000
89 P A -1.3450
90 E A -1.3588
91 Q A 0.0000
92 L A -0.2126
93 I A -0.0451
94 T A -0.8286
95 G A -1.5731
96 K A -2.7867
97 E A -2.8772
98 D A -2.8669
99 A A -1.4918
100 A A -0.8562
101 N A -0.4948
102 N A 0.0000
103 Y A -0.0461
104 A A 0.0000
105 R A 0.0000
106 G A 0.0000
107 H A -0.5399
108 Y A 0.5898
109 T A -0.3810
110 I A -1.1714
111 G A 0.0000
112 K A -2.0747
113 E A -2.7531
114 I A 0.0000
115 I A 0.0000
116 D A -2.6490
117 P A -1.9269
118 V A 0.0000
119 L A -1.6604
120 D A -2.0133
121 R A -1.8134
122 I A 0.0000
123 R A -3.4829
124 K A -3.1452
125 L A 0.0000
126 S A -1.9324
127 D A -2.6523
128 Q A -1.6686
129 C A -0.3028
130 T A -0.2227
131 G A -0.2745
132 L A -0.5298
133 Q A -0.7698
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 -0.2809
144 G A -0.6185
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 -0.6526
153 L A 0.0000
154 M A 0.0000
155 E A -1.1759
156 R A -0.9297
157 L A 0.0000
158 S A 0.0000
159 V A 0.1593
160 D A -1.3437
161 Y A -1.2242
162 G A -1.2335
163 K A -2.1860
164 K A -1.7085
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 -0.0669
174 A A 0.0000
175 P A 0.0000
176 Q A 0.3267
177 V A 1.2798
178 S A 0.4866
179 T A 0.0000
180 A A 0.4305
181 V A 0.0000
182 V A 0.6048
183 E A -0.1244
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 -0.5603
190 T A 0.0000
191 T A 0.0000
192 H A -1.3102
193 T A -0.6363
194 T A 0.0000
195 L A 0.0000
196 E A -1.3311
197 H A -1.2683
198 S A -0.9864
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 0.0000
207 E A -0.4754
208 A A 0.0000
209 I A 0.0000
210 Y A -0.2358
211 D A -1.3625
212 I A 0.0000
213 C A 0.0000
214 R A -1.9667
215 R A -2.5711
216 N A -1.4376
217 L A -0.0790
218 D A -0.5780
219 I A 0.6242
220 E A -1.4394
221 R A -1.4537
222 P A -0.4636
223 T A 0.2987
224 Y A 1.1703
225 T A -0.0550
226 N A 0.0000
227 L A 0.0000
228 N A -0.1865
229 R A -0.1847
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 0.0000
239 T A 0.0000
240 A A 0.0000
241 S A 0.0000
242 L A 0.0000
243 R A -0.6516
244 F A 0.0000
245 D A -1.7974
246 G A -0.9680
247 A A -0.0755
248 L A 0.1549
249 N A 0.0000
250 V A 0.0000
251 D A -0.3093
252 L A 0.0000
253 T A -0.5919
254 E A -0.4675
255 F A 0.0000
256 Q A 0.0000
257 T A -0.7756
258 N A 0.0000
259 L A 0.0000
260 V A 0.0000
261 P A 0.0000
262 Y A 0.0000
263 P A 0.0000
264 R A -1.5897
265 I A 0.0000
266 H A 0.0000
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 0.0000
279 E A -1.2455
280 K A -1.1451
281 A A 0.0000
282 Y A -0.4079
283 H A -1.2859
284 E A -1.4360
285 Q A -1.5178
286 L A -0.9756
287 S A -0.8867
288 V A 0.0000
289 A A -1.1990
290 E A -1.1856
291 I A 0.0000
292 T A 0.0000
293 N A -1.1907
294 A A -0.7564
295 C A 0.0000
296 F A 0.0000
297 E A -1.4167
298 P A -0.9399
299 A A -0.5326
300 N A -1.1262
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.5516
305 C A -1.6878
306 D A -2.4471
307 P A -1.9490
308 R A -1.6006
309 H A -0.9298
310 G A -0.2334
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 -1.4113
323 V A 0.3914
324 V A 0.0000
325 P A -1.3942
326 K A -2.7436
327 D A -2.7414
328 V A 0.0000
329 N A -2.2721
330 A A -1.7530
331 A A 0.0000
332 I A 0.0000
333 A A -1.3225
334 A A -1.6130
335 I A 0.0000
336 K A -2.4722
337 T A -2.3452
338 K A -3.4682
339 R A -3.3919
340 S A -1.8037
341 I A 0.0000
342 Q A -1.5147
343 F A 0.0190
344 V A 1.1427
345 D A -0.4181
346 W A -0.3997
347 C A 0.0000
348 P A 0.0000
349 T A -0.4214
350 G A 0.0000
351 F A 0.1588
352 K A -0.6655
353 V A 0.1454
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A -0.5740
358 Q A -0.9072
359 P A 0.0000
360 P A -0.6458
361 T A 0.0000
362 V A -0.1762
363 V A -0.0750
364 P A -0.4361
365 G A -0.9110
366 G A -1.1116
367 D A 0.0000
368 L A 0.0000
369 A A -1.1339
370 K A -2.0372
371 V A 0.0000
372 Q A -1.4735
373 R A -1.2672
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 0.0000
386 E A -1.2973
387 A A 0.0000
388 W A 0.0000
389 A A -0.9265
390 R A -1.3066
391 L A 0.0000
392 D A -1.7054
393 H A -1.7380
394 K A -0.6618
395 F A 0.0000
396 D A -1.5838
397 L A -0.3585
398 M A 0.0000
399 Y A -0.6491
400 A A -0.8661
401 K A -1.9030
402 R A -2.1161
403 A A -0.6954
404 F A 0.3878
405 V A 0.0000
406 H A -0.8489
407 W A 0.5945
408 Y A 0.0000
409 V A -0.2584
410 G A -0.5510
411 E A -0.7088
412 G A -0.5184
413 M A 0.0000
414 E A -1.3231
415 E A -1.5561
416 G A -1.5337
417 E A -2.0000
418 F A 0.0000
419 S A -2.4900
420 E A -3.4388
421 A A 0.0000
422 R A -3.2521
423 E A -3.5190
424 D A -3.0320
425 M A 0.0000
426 A A -2.0538
427 A A -1.9966
428 L A 0.0000
429 E A -2.0616
430 K A -2.7020
431 D A -2.5201
432 Y A 0.0000
433 E A -1.8022
434 E A -1.8143
435 V A 0.0000
436 G A 0.0000
437 I A 1.0546
438 D A -0.2928
439 S A -1.1757
440 Y A -1.0230
441 E A -2.7410
442 D A -3.3684
443 E A -3.2590
444 D A -3.1175
445 E A -3.1950
446 G A -2.6141
447 E A -2.1583
448 E A -2.4561
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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, -0.6241 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 -0.6241 View CSV PDB
model_10 -0.6432 View CSV PDB
model_2 -0.6549 View CSV PDB
model_6 -0.6613 View CSV PDB
model_9 -0.665 View CSV PDB
model_0 -0.6695 View CSV PDB
CABS_average -0.6771 View CSV PDB
model_3 -0.6865 View CSV PDB
model_5 -0.6872 View CSV PDB
model_7 -0.6883 View CSV PDB
model_11 -0.6892 View CSV PDB
model_4 -0.7268 View CSV PDB
model_1 -0.7294 View CSV PDB
input -0.7431 View CSV PDB