Project name: LacBcELK16

Status: done

Started: 2021-03-01 04:55:43
Settings
Chain sequence(s) A: MELEKFVDPMPIMKTAIPKKTSKDGDYYEIEMKEFSQKLHRDLNPTRLWGYDGQFPGPTIEVMRGKPARIKWMNNLPDTHFLPIDRSIHHVAHEPEVRTVVHLHGSETTPASDGYPEAWFTKDFAEVGSFFEQETYEYPNDQRAATLWYHDHAMGITRLNVYAGLSGLYIIRDPREEQLNLPKGEFDIPLLIQDRSFNDDGSLFYPAQPANPAPNLPNPSVLPFFVGDTILVNGKVWPYLQVEPRKYRFRILNGSNSRSYQLALDSEAPFYQIASDGGLLRRTVSLQAFDIRPAERIEAIIDFSKFEGQTITLKNNASTDATADVMQFQVVLPLSGEDTSIIPQNLSYIPSLQQNDVKRIRNLKISGTTDEYGRPLLLLNNKLWSDPVEEKPCLGTTEIWSFVNVTNVPHPMHIHLVQFQLLDHRAFNVELYNENGQIELVGPTIPPKINERGWKDTITAPAGQITRVIARFAPFSGYYVWHCHILEHEDYDMMRPFVVIDPKTEKERRLEAAAKEAAAKGGGSGGGSLELELKLKLELELKLK
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]                                                (00:01:54)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:01:54)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:01:54)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:01:54)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:56)
[INFO]       CABS:     Running CABS flex simulation                                                (01:14:45)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (07:44:49)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (07:45:04)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (07:45:23)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (07:45:42)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (07:46:01)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (07:46:20)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (07:46:38)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (07:46:55)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (07:47:13)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (07:47:32)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (07:47:51)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (07:48:12)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (07:48:30)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (07:48:47)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (07:48:50)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (07:48:51)
[INFO]       Main:     Simulation completed successfully.                                          (07:49:09)
Show buried residues

Minimal score value
-3.6061
Maximal score value
2.0747
Average score
-0.5128
Total score value
-278.99

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 0.7926
2 E A -0.1442
3 L A 0.8809
4 E A -0.7282
5 K A -0.7315
6 F A 0.1593
7 V A -0.3441
8 D A -1.4290
9 P A 0.0000
10 M A 0.1065
11 P A 0.0540
12 I A 0.4803
13 M A 0.1200
14 K A -0.7596
15 T A -0.2763
16 A A 0.0000
17 I A -0.4428
18 P A -1.1996
19 K A -2.4767
20 K A -2.4431
21 T A -1.9320
22 S A -1.9400
23 K A -2.8390
24 D A -2.8116
25 G A -2.1508
26 D A 0.0000
27 Y A -1.9523
28 Y A 0.0000
29 E A -2.2145
30 I A 0.0000
31 E A -1.6058
32 M A 0.0000
33 K A -1.2728
34 E A 0.0000
35 F A -0.1415
36 S A -0.9739
37 Q A -1.6765
38 K A -2.0583
39 L A -1.7622
40 H A -1.7973
41 R A -2.7252
42 D A -2.4074
43 L A -1.0585
44 N A 0.0000
45 P A -1.9693
46 T A 0.0000
47 R A 0.0000
48 L A 0.3094
49 W A 0.0000
50 G A 0.0000
51 Y A 0.0000
52 D A -2.2119
53 G A -0.9623
54 Q A -0.8591
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 -0.4754
62 V A 0.0000
63 M A -0.5782
64 R A -1.3250
65 G A -1.4235
66 K A -1.6249
67 P A -1.4084
68 A A 0.0000
69 R A -1.9116
70 I A 0.0000
71 K A 0.0000
72 W A 0.0000
73 M A -0.5725
74 N A 0.0000
75 N A -0.8256
76 L A -1.0258
77 P A -0.9910
78 D A -1.2923
79 T A -0.3874
80 H A 0.0000
81 F A 2.0708
82 L A 1.3072
83 P A 0.3242
84 I A -0.7033
85 D A -2.5133
86 R A -2.5751
87 S A -1.5630
88 I A -0.9045
89 H A -1.2676
90 H A -0.5278
91 V A 0.8029
92 A A 0.1544
93 H A -0.8117
94 E A -2.0328
95 P A -1.7801
96 E A -2.2271
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 0.0000
107 E A 0.0000
108 T A 0.0000
109 T A -0.5763
110 P A 0.0000
111 A A 0.0000
112 S A -0.2155
113 D A 0.0000
114 G A 0.0000
115 Y A 0.0000
116 P A 0.0000
117 E A -0.6247
118 A A -0.1061
119 W A 0.2489
120 F A 0.0000
121 T A 0.0000
122 K A -0.5866
123 D A 0.0000
124 F A 0.0000
125 A A 0.0000
126 E A 0.0000
127 V A -0.6318
128 G A -0.7195
129 S A -0.4993
130 F A 0.2754
131 F A 0.0247
132 E A -1.1347
133 Q A -1.6641
134 E A -0.9888
135 T A -1.1770
136 Y A 0.0000
137 E A -1.3513
138 Y A 0.0000
139 P A -0.7294
140 N A 0.0000
141 D A -0.8593
142 Q A 0.0000
143 R A 0.0000
144 A A 0.0000
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 0.2190
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 -0.1871
170 I A 0.0000
171 I A 0.0000
172 R A -1.4728
173 D A 0.0000
174 P A -1.3407
175 R A -1.8741
176 E A -2.4290
177 E A -1.7032
178 Q A 0.0000
179 L A -0.8010
180 N A -0.9193
181 L A -0.6516
182 P A -1.2393
183 K A -2.0705
184 G A -1.6755
185 E A -1.7866
186 F A -0.7562
187 D A -0.4527
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 -1.2549
198 N A -2.3303
199 D A -3.1009
200 D A -3.1217
201 G A -1.3942
202 S A -1.0506
203 L A 0.0000
204 F A 0.0000
205 Y A 0.9615
206 P A 0.9098
207 A A 0.2245
208 Q A 0.0000
209 P A -0.9366
210 A A 0.0000
211 N A -1.4337
212 P A -0.7172
213 A A 0.0000
214 P A -1.0086
215 N A -0.9392
216 L A 0.7299
217 P A 0.2393
218 N A 0.0000
219 P A 0.1178
220 S A 0.0742
221 V A 0.0000
222 L A 0.9853
223 P A 0.0000
224 F A 2.0747
225 F A 0.0000
226 V A 0.6238
227 G A 0.0000
228 D A -1.0711
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 -1.4891
236 V A 0.0000
237 W A 0.0000
238 P A 0.0000
239 Y A -0.0163
240 L A 0.0000
241 Q A -1.2053
242 V A 0.0000
243 E A -2.0601
244 P A -1.4294
245 R A -1.7177
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 -0.0300
258 R A 0.0000
259 S A -0.6909
260 Y A 0.0000
261 Q A -1.2517
262 L A 0.0000
263 A A -1.2016
264 L A -1.4788
265 D A -2.4469
266 S A -1.7936
267 E A -2.2303
268 A A 0.0000
269 P A -1.0374
270 F A 0.0000
271 Y A 0.1489
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 0.0000
280 L A 0.0000
281 R A -1.9169
282 R A -2.4696
283 T A 0.0000
284 V A -0.9009
285 S A -0.6396
286 L A 0.0000
287 Q A -1.6675
288 A A -1.1419
289 F A 0.0000
290 D A -1.3584
291 I A 0.0000
292 R A -0.7054
293 P A 0.0000
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 0.0000
303 F A -1.2214
304 S A 0.0000
305 K A -2.7553
306 F A 0.0000
307 E A -2.4339
308 G A -1.7611
309 Q A -2.1096
310 T A -1.4062
311 I A 0.0000
312 T A -1.1748
313 L A 0.0000
314 K A -1.4324
315 N A 0.0000
316 N A -1.0583
317 A A -0.7458
318 S A -0.4696
319 T A -0.0646
320 D A -0.5897
321 A A -0.3903
322 T A -0.6903
323 A A 0.0000
324 D A -0.8535
325 V A 0.0000
326 M A 0.0000
327 Q A 0.0000
328 F A 0.0000
329 Q A -1.2847
330 V A 0.0000
331 V A -1.3824
332 L A 0.0000
333 P A -1.5220
334 L A -0.9504
335 S A -1.0659
336 G A -1.3773
337 E A -1.7300
338 D A -2.4897
339 T A -0.8145
340 S A 0.5599
341 I A 2.0364
342 I A 1.0895
343 P A -0.0432
344 Q A -0.7300
345 N A -1.6958
346 L A 0.0000
347 S A -0.4306
348 Y A 0.0000
349 I A 1.7632
350 P A 0.5197
351 S A 0.2797
352 L A 0.2579
353 Q A -0.7364
354 Q A -1.4010
355 N A -1.7566
356 D A -1.0050
357 V A 0.3186
358 K A -1.5304
359 R A -0.9333
360 I A 0.8011
361 R A -0.6481
362 N A -1.3479
363 L A 0.0000
364 K A -1.1460
365 I A 0.0000
366 S A 0.0000
367 G A 0.0000
368 T A -1.4041
369 T A 0.0000
370 D A -2.3892
371 E A -0.8621
372 Y A 0.5049
373 G A -0.5624
374 R A -1.3325
375 P A 0.0000
376 L A 0.0000
377 L A 0.0000
378 L A -0.3270
379 L A 0.0000
380 N A -1.8021
381 N A -1.5647
382 K A 0.0000
383 L A 0.5974
384 W A 0.6578
385 S A 0.0122
386 D A -0.4104
387 P A 0.0000
388 V A 0.0000
389 E A 0.0000
390 E A -1.0142
391 K A 0.0000
392 P A 0.0000
393 C A -0.5694
394 L A 0.0266
395 G A -0.8924
396 T A 0.0000
397 T A 0.0000
398 E A 0.0000
399 I A 0.1992
400 W A 0.0000
401 S A 0.0000
402 F A 0.0000
403 V A 0.0113
404 N A 0.0000
405 V A 0.0000
406 T A -1.8817
407 N A -1.5825
408 V A 0.0000
409 P A -0.4215
410 H A 0.0000
411 P A 0.0000
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 -0.1416
419 F A 0.0000
420 Q A 0.0000
421 L A 0.0000
422 L A 0.2833
423 D A -0.2976
424 H A 0.0000
425 R A -0.3158
426 A A 0.3675
427 F A 0.3752
428 N A -0.8570
429 V A -0.8775
430 E A -2.1592
431 L A 0.0000
432 Y A 0.0000
433 N A -1.9150
434 E A -2.3826
435 N A -2.5538
436 G A -1.8332
437 Q A -1.3372
438 I A 0.5262
439 E A 0.6402
440 L A 1.8383
441 V A 1.0271
442 G A 0.1380
443 P A 0.1485
444 T A 0.2517
445 I A 1.0451
446 P A 0.0217
447 P A -0.7399
448 K A -1.3633
449 I A -0.6693
450 N A -1.4954
451 E A -2.3393
452 R A -1.9564
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 -0.3741
460 A A 0.0000
461 P A -0.3176
462 A A -0.5063
463 G A 0.0000
464 Q A 0.0000
465 I A 0.1808
466 T A 0.0000
467 R A -0.9772
468 V A 0.0000
469 I A 0.0000
470 A A 0.0000
471 R A 0.0000
472 F A 0.0000
473 A A -0.2019
474 P A -0.1473
475 F A 0.0970
476 S A -0.2005
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 -0.2450
492 D A 0.0693
493 M A 0.0000
494 M A 0.0000
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 -1.2137
502 P A -1.9793
503 K A -2.7418
504 T A -2.6333
505 E A -3.2272
506 K A -3.6061
507 E A -3.2892
508 R A 0.0000
509 R A -2.7841
510 L A -0.9362
511 E A 0.0000
512 A A -1.2222
513 A A -0.7448
514 A A -0.6767
515 K A 0.0000
516 E A -2.3405
517 A A -0.8868
518 A A -1.0573
519 A A -1.5562
520 K A -2.6343
521 G A -2.1886
522 G A -1.7526
523 G A -1.3384
524 S A -0.8195
525 G A -1.0159
526 G A -1.0346
527 G A 0.0000
528 S A -1.0522
529 L A 0.0000
530 E A -1.6782
531 L A 0.0000
532 E A -1.9030
533 L A -1.1535
534 K A -1.8846
535 L A -1.1374
536 K A -1.8995
537 L A 0.0000
538 E A -1.7352
539 L A 0.0000
540 E A 0.0000
541 L A -1.5793
542 K A -2.0846
543 L A -1.2350
544 K A -2.1280
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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, -0.5128 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_7 -0.5128 View CSV PDB
model_5 -0.5226 View CSV PDB
model_0 -0.5348 View CSV PDB
model_10 -0.5471 View CSV PDB
model_9 -0.5514 View CSV PDB
model_6 -0.552 View CSV PDB
model_2 -0.5552 View CSV PDB
model_11 -0.5574 View CSV PDB
model_4 -0.5656 View CSV PDB
model_1 -0.5816 View CSV PDB
model_3 -0.5865 View CSV PDB
model_8 -0.608 View CSV PDB
input -0.6789 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018