Project name: mj_TB_wt_dynamic [mutate: AT383A]

Status: done

Started: 2025-02-25 05:50:44
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 AT383A
Energy difference between WT (input) and mutated protein (by FoldX) 7.69931 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                                                       (00:14:57)
[INFO]       CABS:     Running CABS flex simulation                                                (00:15:11)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:50:16)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:50:20)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:50:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:50:26)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:50:29)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:50:32)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:50:35)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:50:38)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:50:41)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:50:44)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:50:47)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:50:51)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:50:54)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:51:03)
[INFO]       Main:     Simulation completed successfully.                                          (01:51:06)
Show buried residues

Minimal score value
-3.935
Maximal score value
1.2408
Average score
-0.6805
Total score value
-304.8658

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 0.1210
2 R A -0.1453
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 -0.5958
12 A A -0.4140
13 G A 0.0000
14 V A 0.0000
15 Q A -0.7574
16 M A -0.4241
17 G A 0.0000
18 N A -0.7176
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -1.1141
23 L A 0.0000
24 Y A 0.0000
25 C A -0.2998
26 L A 0.2683
27 E A -0.3894
28 H A 0.0000
29 G A -0.3285
30 I A 0.2251
31 Q A 0.0000
32 P A -0.9461
33 D A -1.6563
34 G A 0.0000
35 Q A -1.3707
36 M A 0.0000
37 P A 0.0000
38 S A 0.0000
39 D A -1.8269
40 K A -1.4097
41 T A -0.3517
42 I A 1.1153
43 G A 0.3130
44 G A -0.2715
45 G A -0.3781
46 D A 0.0000
47 D A -0.6832
48 S A 0.0000
49 F A 0.0000
50 T A -0.5057
51 T A 0.0000
52 F A 0.0000
53 F A 0.0234
54 C A -0.2418
55 E A -1.4029
56 T A -1.0916
57 G A -0.9613
58 A A -0.6795
59 G A -1.1128
60 K A -1.4056
61 H A -1.1032
62 V A -0.7914
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 -2.2767
72 P A 0.0000
73 T A -2.0520
74 V A 0.0000
75 I A 0.0000
76 D A -3.8551
77 E A -3.9350
78 I A 0.0000
79 R A -3.8834
80 N A -3.4857
81 G A -2.7080
82 P A -2.3716
83 Y A -2.0449
84 R A -2.2789
85 Q A -1.4104
86 L A 0.0000
87 F A 0.0000
88 H A -1.7722
89 P A -1.9077
90 E A -2.1420
91 Q A 0.0000
92 L A -0.9542
93 I A -0.4892
94 T A -0.8023
95 G A -1.5605
96 K A -2.9451
97 E A -2.8136
98 D A -3.3528
99 A A 0.0000
100 A A -2.0487
101 N A -1.7760
102 N A 0.0000
103 Y A 0.0000
104 A A -1.1471
105 R A -2.7041
106 G A 0.0000
107 H A -1.5455
108 Y A -0.6983
109 T A -0.5869
110 I A -1.0267
111 G A 0.0000
112 K A -1.7650
113 E A -2.4594
114 I A 0.0000
115 I A 0.0000
116 D A -2.6814
117 P A -1.8446
118 V A 0.0000
119 L A 0.0000
120 D A -2.3148
121 R A -2.3257
122 I A 0.0000
123 R A -2.7748
124 K A -2.8039
125 L A 0.0000
126 S A 0.0000
127 D A -2.4713
128 Q A -1.5003
129 C A -0.3137
130 T A -0.3003
131 G A -0.0719
132 L A 0.7074
133 Q A -0.4769
134 G A 0.0000
135 F A -0.0341
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 -0.1690
144 G A 0.0000
145 T A 0.0000
146 G A 0.0000
147 S A 0.0000
148 G A -0.1007
149 F A 0.0000
150 T A 0.0000
151 S A -0.4841
152 L A -0.7087
153 L A 0.0000
154 M A 0.0000
155 E A -1.2033
156 R A -1.1118
157 L A 0.0000
158 S A 0.0000
159 V A 0.5632
160 D A -0.7523
161 Y A -0.1729
162 G A -1.0626
163 K A -2.2053
164 K A -1.6604
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 -0.3488
175 P A -0.2633
176 Q A -0.0129
177 V A 1.1774
178 S A 0.3603
179 T A 0.1424
180 A A 0.2888
181 V A -0.2851
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 -0.7077
190 T A 0.0000
191 T A 0.0000
192 H A 0.0000
193 T A -0.7848
194 T A 0.0000
195 L A 0.0000
196 E A -1.3924
197 H A -1.2141
198 S A 0.0000
199 D A 0.0000
200 C A 0.0000
201 A A 0.0000
202 F A 0.1710
203 M A 0.0000
204 V A 0.0000
205 D A -0.4781
206 N A -0.4774
207 E A -0.8295
208 A A 0.0000
209 I A 0.0000
210 Y A -0.4834
211 D A -1.5263
212 I A 0.0000
213 C A 0.0000
214 R A -2.3946
215 R A -2.3710
216 N A -1.8954
217 L A -1.8191
218 D A -2.0147
219 I A 0.0000
220 E A -2.7309
221 R A -2.4991
222 P A -1.2644
223 T A -0.7112
224 Y A 0.6206
225 T A -0.0927
226 N A 0.0000
227 L A 0.1670
228 N A 0.0000
229 R A -0.4115
230 L A 0.0000
231 I A 0.0000
232 S A 0.0000
233 Q A 0.0000
234 I A 0.1324
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 0.0482
241 S A 0.0000
242 L A 0.0000
243 R A 0.0000
244 F A -0.3505
245 D A -1.2884
246 G A -0.8512
247 A A 0.0607
248 L A 0.3127
249 N A -0.8852
250 V A -0.3516
251 D A 0.0000
252 L A 0.0000
253 T A -0.2622
254 E A -0.6598
255 F A 0.0000
256 Q A 0.0000
257 T A -1.0723
258 N A -1.0280
259 L A 0.0000
260 V A 0.0000
261 P A -0.9908
262 Y A 0.0000
263 P A 0.0000
264 R A -1.3945
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 -1.4185
280 K A -1.2863
281 A A 0.0000
282 Y A -1.0351
283 H A -1.2448
284 E A 0.0000
285 Q A -1.7018
286 L A 0.0000
287 S A -1.0393
288 V A 0.0000
289 A A -1.1074
290 E A -1.4409
291 I A 0.0000
292 T A 0.0000
293 N A -1.1244
294 A A 0.0000
295 C A 0.0000
296 F A 0.0000
297 E A -1.3076
298 P A -0.8394
299 A A -0.7131
300 N A 0.0000
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.3824
305 C A 0.0000
306 D A -2.5064
307 P A -2.3716
308 R A -2.8936
309 H A -2.1114
310 G A -1.7346
311 K A -1.0339
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 -0.8282
323 V A 0.2349
324 V A 1.2408
325 P A -0.5180
326 K A -2.1548
327 D A -2.0519
328 V A 0.0000
329 N A -1.5828
330 A A -1.4059
331 A A 0.0000
332 I A -0.9775
333 A A -1.2105
334 A A -1.2634
335 I A 0.0000
336 K A -2.6704
337 T A -2.2440
338 K A -3.2760
339 R A -3.4533
340 S A -2.2222
341 I A 0.0000
342 Q A -1.9001
343 F A -0.5527
344 V A -0.2418
345 D A -0.8808
346 W A 0.3307
347 C A 0.3599
348 P A 0.0000
349 T A -0.0997
350 G A 0.0000
351 F A 0.3285
352 K A -0.4874
353 V A 0.0479
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A 0.0952
358 Q A -0.4555
359 P A 0.0000
360 P A -0.4506
361 T A 0.0000
362 V A -0.5900
363 V A 0.0000
364 P A -0.8204
365 G A -1.1991
366 G A -1.8747
367 D A -2.5992
368 L A 0.0000
369 A A -1.7033
370 K A -2.5449
371 V A 0.0000
372 Q A -1.3228
373 R A -0.9157
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 T A 0.0000 mutated: AT383A
384 I A 0.0000
385 A A 0.0000
386 E A -1.6488
387 A A 0.0000
388 W A 0.0000
389 A A -1.2893
390 R A -1.7414
391 L A 0.0000
392 D A -1.9537
393 H A -1.9826
394 K A -1.1900
395 F A 0.0000
396 D A -2.0693
397 L A -0.6417
398 M A 0.0000
399 Y A -0.8734
400 A A -1.0251
401 K A -2.1640
402 R A -2.3315
403 A A -1.1265
404 F A 0.0000
405 V A 0.0000
406 H A -1.1454
407 W A 0.0596
408 Y A 0.0000
409 V A -0.4991
410 G A -0.7352
411 E A -1.3369
412 G A -1.0914
413 M A -1.1582
414 E A -2.4171
415 E A -3.2214
416 G A -2.7450
417 E A -3.1409
418 F A 0.0000
419 S A -2.9712
420 E A -3.7160
421 A A 0.0000
422 R A -3.4545
423 E A -3.3639
424 D A -2.5101
425 M A 0.0000
426 A A -1.8932
427 A A -1.7447
428 L A 0.0000
429 E A -2.0133
430 K A -2.5111
431 D A 0.0000
432 Y A 0.0000
433 E A -2.8626
434 E A -1.7250
435 V A 0.0000
436 G A 0.0000
437 I A 0.1417
438 D A -0.9420
439 S A -0.4198
440 Y A 0.1999
441 E A -1.1683
442 D A -1.9453
443 E A -2.7368
444 D A -3.1587
445 E A -3.6001
446 G A -2.8311
447 E A -2.8322
448 E A -2.1425
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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, -0.6805 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_1 -0.6805 View CSV PDB
model_5 -0.7183 View CSV PDB
model_6 -0.7209 View CSV PDB
model_3 -0.7327 View CSV PDB
input -0.7424 View CSV PDB
model_2 -0.7427 View CSV PDB
CABS_average -0.7444 View CSV PDB
model_8 -0.7474 View CSV PDB
model_11 -0.7565 View CSV PDB
model_9 -0.7602 View CSV PDB
model_10 -0.7649 View CSV PDB
model_0 -0.7669 View CSV PDB
model_7 -0.7678 View CSV PDB
model_4 -0.7738 View CSV PDB