Project name: mj_TB_wt_dynamic [mutate: GV43A]

Status: done

Started: 2025-02-25 05:49:00
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 GV43A
Energy difference between WT (input) and mutated protein (by FoldX) 24.329 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]                                                (00:00:08)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:08)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:08)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:08)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:09)
[INFO]       FoldX:    Building mutant model                                                       (00:15:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:15:15)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:46:04)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:46:07)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:46:11)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:46:14)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:46:18)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:46:22)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:46:24)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:46:28)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:46:31)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:46:34)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:46:38)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:46:42)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:46:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:46:55)
[INFO]       Main:     Simulation completed successfully.                                          (01:46:58)
Show buried residues

Minimal score value
-5.0574
Maximal score value
2.4486
Average score
-0.6365
Total score value
-285.1634

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 0.0303
2 R A -0.6861
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 -0.8503
12 A A -0.3235
13 G A 0.0000
14 V A 0.0000
15 Q A -0.6402
16 M A 0.0000
17 G A 0.0000
18 N A -0.8136
19 A A 0.0000
20 C A 0.0000
21 W A 0.0000
22 E A -0.4161
23 L A 0.0000
24 Y A 0.0000
25 C A 0.7540
26 L A 0.9396
27 E A 0.0000
28 H A -0.3128
29 G A 0.0072
30 I A 0.8621
31 Q A -1.0473
32 P A -1.3400
33 D A -2.3547
34 G A -1.4517
35 Q A -1.0461
36 M A 0.0000
37 P A -1.0978
38 S A -1.4549
39 D A -2.5610
40 K A -2.2509
41 T A -0.3060
42 I A 1.8501
43 V A 2.4486 mutated: GV43A
44 G A 1.0300
45 G A 0.1317
46 D A 0.0000
47 D A -1.7544
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 0.0130
54 C A 0.0000
55 E A -0.9230
56 T A -0.6682
57 G A -0.7822
58 A A -0.6014
59 G A -1.4384
60 K A -1.8482
61 H A -1.3024
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 -2.4979
72 P A -1.7047
73 T A -1.3022
74 V A 0.0000
75 I A 0.0000
76 D A -3.1919
77 E A -3.1814
78 I A 0.0000
79 R A -2.8512
80 N A -2.7502
81 G A -1.7471
82 P A -1.2037
83 Y A -0.0399
84 R A -1.2276
85 Q A -0.7497
86 L A 0.0000
87 F A 0.0000
88 H A 0.0000
89 P A -1.3554
90 E A -2.2304
91 Q A 0.0000
92 L A -0.5080
93 I A -0.3526
94 T A -1.2542
95 G A -2.2885
96 K A -3.4116
97 E A -3.6656
98 D A -3.5137
99 A A 0.0000
100 A A -1.5356
101 N A 0.0000
102 N A -0.6101
103 Y A 0.0000
104 A A 0.0000
105 R A -1.3845
106 G A 0.0000
107 H A -1.2745
108 Y A -0.4418
109 T A -0.9241
110 I A -1.6059
111 G A 0.0000
112 K A -2.3754
113 E A -2.4945
114 I A 0.0000
115 I A 0.0000
116 D A -2.1818
117 P A -1.8785
118 V A 0.0000
119 L A -1.7075
120 D A -2.7329
121 R A -2.6714
122 I A 0.0000
123 R A -3.6230
124 K A -3.9717
125 L A 0.0000
126 S A 0.0000
127 D A -3.2106
128 Q A -2.0382
129 C A -0.6474
130 T A -0.5744
131 G A -0.2863
132 L A 0.8167
133 Q A 0.0778
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 -0.1208
145 T A -0.7207
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 -0.4595
152 L A -0.7742
153 L A 0.0000
154 M A 0.0000
155 E A -1.6159
156 R A -1.1337
157 L A 0.0000
158 S A -0.7967
159 V A 0.1470
160 D A 0.0000
161 Y A -0.2016
162 G A -0.6435
163 K A -1.5204
164 K A -2.7811
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 -0.4052
175 P A -0.1024
176 Q A 0.4103
177 V A 1.5510
178 S A 0.6999
179 T A 0.4532
180 A A 0.3270
181 V A 0.1165
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 -1.4701
193 T A -0.9403
194 T A 0.0000
195 L A 0.0000
196 E A -2.4256
197 H A 0.0000
198 S A 0.0000
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 -0.8744
208 A A 0.0000
209 I A 0.0000
210 Y A -0.4479
211 D A -1.3245
212 I A 0.0000
213 C A 0.0000
214 R A -1.9631
215 R A -1.0550
216 N A 0.0000
217 L A 0.1599
218 D A -1.1296
219 I A -1.1831
220 E A -2.4442
221 R A -2.5854
222 P A -1.3872
223 T A 0.0000
224 Y A 0.1909
225 T A -0.4282
226 N A -0.5972
227 L A 0.0000
228 N A 0.0000
229 R A -0.6253
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 0.0000
244 F A -1.0746
245 D A -1.7695
246 G A -1.0596
247 A A 0.0528
248 L A 0.6024
249 N A -0.8745
250 V A 0.0000
251 D A -0.8486
252 L A 0.0000
253 T A -0.5502
254 E A -1.1257
255 F A 0.0000
256 Q A 0.0000
257 T A -1.1746
258 N A -1.1499
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 -2.2361
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 -0.5994
279 E A -1.0500
280 K A -0.7972
281 A A 0.0000
282 Y A -0.2381
283 H A -1.3083
284 E A -1.6179
285 Q A -1.6170
286 L A 0.0000
287 S A -0.8842
288 V A 0.0000
289 A A -1.4510
290 E A -1.7446
291 I A 0.0000
292 T A 0.0000
293 N A -2.2424
294 A A -1.4038
295 C A 0.0000
296 F A 0.0000
297 E A -2.3721
298 P A -1.7941
299 A A -1.2946
300 N A -1.5994
301 Q A 0.0000
302 M A 0.0000
303 V A 0.0000
304 K A -1.3398
305 C A 0.0000
306 D A -2.1862
307 P A -1.7555
308 R A -1.7787
309 H A -0.8944
310 G A -0.2295
311 K A 0.0497
312 Y A 0.0000
313 M A 0.0000
314 A A 0.0309
315 C A 0.0000
316 C A -0.2127
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 -0.7637
323 V A 0.2704
324 V A -0.1742
325 P A -1.2046
326 K A -2.3488
327 D A -1.9501
328 V A 0.0000
329 N A -1.9047
330 A A -1.1812
331 A A 0.0000
332 I A -1.0363
333 A A -0.6794
334 A A -1.0373
335 I A 0.0000
336 K A -1.8224
337 T A -0.9905
338 K A 0.0000
339 R A -2.1218
340 S A -0.8684
341 I A 1.1462
342 Q A 0.7278
343 F A 1.5896
344 V A 1.3285
345 D A -0.0011
346 W A 0.5616
347 C A 0.6452
348 P A 0.1774
349 T A -0.2134
350 G A -0.6640
351 F A 0.0000
352 K A -0.8472
353 V A 0.0000
354 G A 0.0000
355 I A 0.0000
356 N A 0.0000
357 Y A 0.4183
358 Q A 0.4567
359 P A 0.0000
360 P A -0.4389
361 T A 0.0000
362 V A -0.5352
363 V A 0.0000
364 P A -0.9422
365 G A -1.0314
366 G A -1.5089
367 D A -1.8508
368 L A 0.0000
369 A A 0.0000
370 K A -0.8963
371 V A 0.0000
372 Q A -0.8831
373 R A -0.8173
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 -1.4916
387 A A -1.0100
388 W A 0.0000
389 A A -1.5667
390 R A -2.2701
391 L A 0.0000
392 D A -2.3400
393 H A -2.3246
394 K A -1.4666
395 F A 0.0000
396 D A -2.1028
397 L A -0.6641
398 M A 0.0000
399 Y A -0.4306
400 A A -0.7513
401 K A -1.8477
402 R A -1.7586
403 A A -0.6520
404 F A 0.3574
405 V A 0.0000
406 H A -1.0345
407 W A 0.7398
408 Y A 0.0000
409 V A -0.9187
410 G A -1.0684
411 E A -1.1123
412 G A -1.4022
413 M A 0.0000
414 E A -2.8571
415 E A -2.5225
416 G A -2.3457
417 E A -2.4325
418 F A 0.0000
419 S A -2.5332
420 E A -3.3850
421 A A 0.0000
422 R A -3.2732
423 E A -3.3905
424 D A -2.7690
425 M A 0.0000
426 A A -2.0092
427 A A -1.7628
428 L A 0.0000
429 E A -1.7466
430 K A -2.1709
431 D A 0.0000
432 Y A 0.0000
433 E A -1.3456
434 E A -1.4347
435 V A 0.0000
436 G A 0.0000
437 I A 1.3184
438 D A -0.3142
439 S A -1.6267
440 Y A 0.0000
441 E A -4.3492
442 D A -4.3846
443 E A -4.3367
444 D A -5.0574
445 E A -4.6337
446 G A -3.7255
447 E A -3.9117
448 E A -3.5093
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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, -0.6365 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_11 -0.6365 View CSV PDB
model_1 -0.655 View CSV PDB
model_6 -0.6782 View CSV PDB
model_5 -0.6787 View CSV PDB
model_7 -0.687 View CSV PDB
model_0 -0.6886 View CSV PDB
model_8 -0.6905 View CSV PDB
CABS_average -0.6913 View CSV PDB
model_4 -0.7042 View CSV PDB
model_2 -0.7073 View CSV PDB
model_10 -0.7073 View CSV PDB
model_9 -0.7216 View CSV PDB
model_3 -0.7403 View CSV PDB
input -0.7425 View CSV PDB