Project name: LacBc18Av15

Status: done

Started: 2021-03-01 04:56:45
Settings
Chain sequence(s) A: MELEKFVDPMPIMKTAIPKKTSKDGDYYEIEMKEFSQKLHRDLNPTRLWGYDGQFPGPTIEVMRGKPARIKWMNNLPDTHFLPIDRSIHHVAHEPEVRTVVHLHGSETTPASDGYPEAWFTKDFAEVGSFFEQETYEYPNDQRAATLWYHDHAMGITRLNVYAGLSGLYIIRDPREEQLNLPKGEFDIPLLIQDRSFNDDGSLFYPAQPANPAPNLPNPSVLPFFVGDTILVNGKVWPYLQVEPRKYRFRILNGSNSRSYQLALDSEAPFYQIASDGGLLRRTVSLQAFDIRPAERIEAIIDFSKFEGQTITLKNNASTDATADVMQFQVVLPLSGEDTSIIPQNLSYIPSLQQNDVKRIRNLKISGTTDEYGRPLLLLNNKLWSDPVEEKPCLGTTEIWSFVNVTNVPHPMHIHLVQFQLLDHRAFNVELYNENGQIELVGPTIPPKINERGWKDTITAPAGQITRVIARFAPFSGYYVWHCHILEHEDYDMMRPFVVIDPKTEKERRLEAAAKEAAAKGGGSGGGSEWLEAFYKEVLKKLEELF
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:01:37)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:01:38)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:01:38)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:39)
[INFO]       CABS:     Running CABS flex simulation                                                (01:05:05)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (07:36:16)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (07:36:36)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (07:36:53)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (07:37:11)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (07:37:27)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (07:37:45)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (07:38:06)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (07:38:26)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (07:38:46)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (07:39:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (07:39:24)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (07:39:41)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (07:40:00)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (07:40:22)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (07:40:24)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (07:40:25)
[INFO]       Main:     Simulation completed successfully.                                          (07:40:42)
Show buried residues

Minimal score value
-3.7296
Maximal score value
2.5494
Average score
-0.484
Total score value
-264.2726

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 M A -1.1006
2 E A -2.0208
3 L A 0.0000
4 E A -1.7929
5 K A -2.1869
6 F A -0.5865
7 V A 0.9541
8 D A 0.0000
9 P A 0.2566
10 M A 0.0000
11 P A -0.1303
12 I A 0.0000
13 M A -0.0530
14 K A -0.7673
15 T A -0.5844
16 A A -0.8377
17 I A 0.0000
18 P A -1.0773
19 K A -1.7195
20 K A -2.4492
21 T A -1.8414
22 S A -2.0922
23 K A -2.8949
24 D A -2.8245
25 G A -2.3471
26 D A 0.0000
27 Y A -1.9091
28 Y A 0.0000
29 E A -1.4850
30 I A 0.0000
31 E A -1.0908
32 M A 0.0000
33 K A -1.0926
34 E A -1.3230
35 F A -0.5967
36 S A -0.8291
37 Q A 0.0000
38 K A -0.9050
39 L A 0.4556
40 H A 0.0000
41 R A -1.8728
42 D A -0.9401
43 L A 0.0000
44 N A -0.7501
45 P A -0.8094
46 T A 0.0000
47 R A -1.5866
48 L A 0.0000
49 W A 0.0000
50 G A 0.0000
51 Y A 0.0000
52 D A -1.0127
53 G A -0.6480
54 Q A -0.5676
55 F A 0.0000
56 P A 0.0000
57 G A 0.0000
58 P A 0.0000
59 T A 0.0000
60 I A 0.0000
61 E A -0.8209
62 V A 0.0000
63 M A -1.2819
64 R A -2.2491
65 G A -1.8485
66 K A -2.2506
67 P A -2.0290
68 A A 0.0000
69 R A -2.6175
70 I A 0.0000
71 K A -1.1254
72 W A 0.0000
73 M A 0.1005
74 N A 0.0000
75 N A -1.6169
76 L A 0.0000
77 P A -1.7561
78 D A -2.1348
79 T A -1.2084
80 H A -0.7136
81 F A 0.8414
82 L A 0.0000
83 P A 0.0000
84 I A 0.0000
85 D A -2.1186
86 R A -2.0671
87 S A 0.0000
88 I A 0.5498
89 H A 0.3646
90 H A 0.6971
91 V A 1.1220
92 A A 0.2888
93 H A -0.9740
94 E A -2.1015
95 P A -1.7570
96 E A -0.9676
97 V A 0.0000
98 R A 0.0000
99 T A 0.0000
100 V A 0.0000
101 V A 0.0000
102 H A 0.0000
103 L A 0.0000
104 H A 0.0000
105 G A 0.0000
106 S A -0.5612
107 E A 0.0000
108 T A 0.1633
109 T A 0.0000
110 P A 0.2660
111 A A -0.1961
112 S A 0.0000
113 D A 0.0000
114 G A 0.0000
115 Y A 0.0000
116 P A 0.0000
117 E A 0.0000
118 A A 0.2197
119 W A 0.2905
120 F A 0.0000
121 T A 0.0000
122 K A -1.3422
123 D A 0.0000
124 F A 0.0000
125 A A 0.0000
126 E A -0.9971
127 V A -0.7257
128 G A -1.0688
129 S A -0.7308
130 F A 0.0000
131 F A -0.9241
132 E A -2.2797
133 Q A -1.8244
134 E A 0.0000
135 T A -1.2418
136 Y A 0.0000
137 E A -1.8572
138 Y A 0.0000
139 P A -1.4987
140 N A 0.0000
141 D A -2.3839
142 Q A 0.0000
143 R A -1.4287
144 A A -0.9194
145 A A 0.0000
146 T A 0.0000
147 L A 0.0000
148 W A 0.0000
149 Y A 0.0000
150 H A 0.0000
151 D A 0.0000
152 H A 0.0000
153 A A 0.0000
154 M A 0.0000
155 G A 0.0000
156 I A 0.0000
157 T A 0.0000
158 R A 0.0000
159 L A 0.0000
160 N A 0.0000
161 V A 0.0000
162 Y A 0.0000
163 A A 0.0000
164 G A 0.0000
165 L A 0.0000
166 S A 0.0000
167 G A 0.0000
168 L A 0.0000
169 Y A 0.0000
170 I A 0.0000
171 I A 0.0000
172 R A -1.9150
173 D A -2.6320
174 P A -2.4394
175 R A -3.3832
176 E A -3.7296
177 E A -3.2804
178 Q A -1.7240
179 L A -0.3239
180 N A -1.1187
181 L A 0.0000
182 P A -0.9960
183 K A -1.4389
184 G A -1.6949
185 E A -1.0227
186 F A -0.5949
187 D A -0.2463
188 I A 0.0000
189 P A 0.0000
190 L A 0.0000
191 L A 0.0000
192 I A 0.0000
193 Q A 0.0000
194 D A 0.0000
195 R A 0.0000
196 S A 0.0000
197 F A 0.1208
198 N A -1.2447
199 D A -2.2875
200 D A -1.7966
201 G A -1.6910
202 S A -1.4549
203 L A 0.0000
204 F A 0.0000
205 Y A 0.0000
206 P A -0.4863
207 A A -0.7100
208 Q A -1.1872
209 P A 0.0000
210 A A 0.0000
211 N A -0.7654
212 P A -0.6087
213 A A 0.0000
214 P A -1.3198
215 N A -1.7641
216 L A -0.2846
217 P A -0.4784
218 N A -0.7743
219 P A -0.5074
220 S A 0.0000
221 V A 1.2216
222 L A 1.0590
223 P A 0.0000
224 F A 1.2915
225 F A 1.7738
226 V A 1.8755
227 G A 0.0000
228 D A -0.2480
229 T A 0.0000
230 I A 0.0000
231 L A 0.0000
232 V A 0.0000
233 N A 0.0000
234 G A 0.0000
235 K A 0.0000
236 V A 0.0000
237 W A 0.2397
238 P A 0.0000
239 Y A -0.1931
240 L A 0.0000
241 Q A -1.1620
242 V A 0.0000
243 E A -2.0104
244 P A -1.3579
245 R A -1.5114
246 K A 0.0000
247 Y A 0.0000
248 R A 0.0000
249 F A 0.0000
250 R A 0.0000
251 I A 0.0000
252 L A 0.0000
253 N A 0.0000
254 G A 0.0000
255 S A 0.0000
256 N A 0.0000
257 S A 0.4131
258 R A 0.0000
259 S A -0.3945
260 Y A 0.0000
261 Q A -0.6521
262 L A 0.0000
263 A A -1.1465
264 L A -1.4764
265 D A -2.2223
266 S A -1.9544
267 E A -2.2971
268 A A 0.0000
269 P A -0.7845
270 F A 0.0000
271 Y A 0.0000
272 Q A 0.0000
273 I A 0.0000
274 A A 0.0000
275 S A 0.0000
276 D A 0.0000
277 G A 0.0000
278 G A 0.0000
279 L A -0.2848
280 L A 0.0000
281 R A -1.1639
282 R A 0.0000
283 T A 0.0000
284 V A 0.0000
285 S A -0.7699
286 L A 0.0000
287 Q A -1.4230
288 A A -1.0190
289 F A 0.0000
290 D A 0.0000
291 I A 0.0000
292 R A -0.3653
293 P A -0.1931
294 A A 0.0000
295 E A 0.0000
296 R A 0.0000
297 I A 0.0000
298 E A 0.0000
299 A A 0.0000
300 I A 0.0000
301 I A 0.0000
302 D A -0.1444
303 F A -0.5218
304 S A -1.5107
305 K A -2.4532
306 F A 0.0000
307 E A -2.7893
308 G A -1.7406
309 Q A -1.5554
310 T A -1.1603
311 I A 0.0000
312 T A -1.3883
313 L A 0.0000
314 K A -2.1111
315 N A 0.0000
316 N A -1.3268
317 A A -0.6403
318 S A -0.3220
319 T A 0.0777
320 D A 0.0000
321 A A -0.2916
322 T A -0.8386
323 A A 0.0000
324 D A -2.4594
325 V A 0.0000
326 M A 0.0000
327 Q A -1.0317
328 F A 0.0000
329 Q A -1.3125
330 V A 0.0000
331 V A -1.1834
332 L A -1.2764
333 P A -0.4166
334 L A 1.0084
335 S A -0.5230
336 G A -1.4229
337 E A -2.7567
338 D A -2.5206
339 T A -1.0530
340 S A -0.2066
341 I A 0.5900
342 I A 1.3744
343 P A -0.1873
344 Q A -1.0636
345 N A -1.0676
346 L A 0.2951
347 S A 0.0769
348 Y A 0.7468
349 I A 1.8562
350 P A 1.2282
351 S A 0.7571
352 L A 1.2576
353 Q A 0.0000
354 Q A -2.0418
355 N A -2.7000
356 D A -2.9931
357 V A -1.2703
358 K A -1.5116
359 R A -0.4385
360 I A 1.0102
361 R A -0.3774
362 N A -1.1426
363 L A 0.0000
364 K A -0.7531
365 I A 0.0000
366 S A 0.0000
367 G A -0.5080
368 T A -1.1274
369 T A -1.6416
370 D A -2.9309
371 E A -2.8589
372 Y A -1.8299
373 G A -1.4297
374 R A -1.3121
375 P A 0.0000
376 L A -0.1439
377 L A 0.0000
378 L A 0.5078
379 L A 0.0000
380 N A 0.0000
381 N A -0.8799
382 K A 0.0000
383 L A 1.7947
384 W A 1.4794
385 S A 0.2941
386 D A -0.5988
387 P A 0.1609
388 V A 0.0000
389 E A -0.7346
390 E A 0.0000
391 K A 0.0000
392 P A 0.0000
393 C A 0.0858
394 L A -0.0608
395 G A -0.9369
396 T A -1.5028
397 T A 0.0000
398 E A 0.0000
399 I A 0.0000
400 W A 0.0000
401 S A -0.3999
402 F A 0.0000
403 V A 0.0000
404 N A 0.0000
405 V A 0.0000
406 T A -0.7139
407 N A -0.6723
408 V A -0.2306
409 P A -0.2910
410 H A 0.0000
411 P A -0.1323
412 M A 0.0000
413 H A 0.0000
414 I A 0.0000
415 H A 0.0000
416 L A 0.0000
417 V A 0.0000
418 Q A -0.5423
419 F A 0.0000
420 Q A 0.0000
421 L A 0.0000
422 L A 0.0000
423 D A -0.9331
424 H A 0.0000
425 R A -0.2605
426 A A 0.3618
427 F A 0.9453
428 N A 0.1227
429 V A 1.1846
430 E A 0.5877
431 L A 0.0000
432 Y A 1.0619
433 N A 0.0000
434 E A -1.2012
435 N A -1.4997
436 G A -0.7987
437 Q A 0.2787
438 I A 1.8632
439 E A 1.7152
440 L A 2.5494
441 V A 2.0671
442 G A 0.7982
443 P A 0.0034
444 T A 0.1394
445 I A 0.4241
446 P A -0.5077
447 P A -0.8923
448 K A -1.1009
449 I A 0.0000
450 N A -1.5444
451 E A -1.1691
452 R A 0.0000
453 G A 0.0000
454 W A 0.0000
455 K A 0.0000
456 D A 0.0000
457 T A 0.0000
458 I A 0.0000
459 T A 0.0000
460 A A 0.0000
461 P A -0.2558
462 A A -0.2094
463 G A 0.0000
464 Q A 0.0000
465 I A 0.0000
466 T A 0.0000
467 R A -0.5406
468 V A 0.0000
469 I A 0.0000
470 A A 0.0000
471 R A -1.0757
472 F A 0.0000
473 A A 0.1716
474 P A 0.7117
475 F A 1.6339
476 S A 0.5918
477 G A 0.0000
478 Y A 0.0000
479 Y A 0.0000
480 V A 0.0000
481 W A 0.0000
482 H A 0.0000
483 C A 0.0000
484 H A 0.0000
485 I A 0.0000
486 L A 0.0000
487 E A 0.0000
488 H A 0.0000
489 E A 0.0000
490 D A 0.0000
491 Y A 0.0000
492 D A 0.1418
493 M A 0.0000
494 M A 0.4313
495 R A 0.0000
496 P A 0.0000
497 F A 0.0000
498 V A 0.0000
499 V A 0.0000
500 I A 0.0000
501 D A -0.7645
502 P A -1.1126
503 K A -2.5670
504 T A 0.0000
505 E A -2.8875
506 K A -3.0869
507 E A 0.0000
508 R A -2.1604
509 R A -2.5069
510 L A -1.1437
511 E A -1.2737
512 A A -1.6159
513 A A -1.0442
514 A A -0.9896
515 K A -1.6198
516 E A -2.5174
517 A A -1.5797
518 A A 0.0000
519 A A -2.0258
520 K A -2.7939
521 G A -2.0688
522 G A -1.4678
523 G A -1.1137
524 S A -1.0275
525 G A -1.2477
526 G A -1.1218
527 G A -1.2799
528 S A -1.1877
529 E A -0.5322
530 W A 0.2037
531 L A 0.0000
532 E A -1.8960
533 A A -0.8001
534 F A -0.9120
535 Y A -1.6570
536 K A -2.3025
537 E A -2.1765
538 V A 0.0000
539 L A -2.1557
540 K A -3.0011
541 K A -2.0479
542 L A -1.4916
543 E A -2.6081
544 E A -2.2600
545 L A -0.0262
546 F A 1.4894
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.484 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 A3D Score
model_1 -0.484 View CSV PDB
model_0 -0.5577 View CSV PDB
model_4 -0.5601 View CSV PDB
model_9 -0.5627 View CSV PDB
model_5 -0.5676 View CSV PDB
model_2 -0.5686 View CSV PDB
model_8 -0.5703 View CSV PDB
model_11 -0.5952 View CSV PDB
model_10 -0.5956 View CSV PDB
model_3 -0.609 View CSV PDB
model_7 -0.6104 View CSV PDB
model_6 -0.6134 View CSV PDB
input -0.6931 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018