Project name: 3aa16a4d2107b9e

Status: done

Started: 2025-02-26 18:49:55
Chain sequence(s) A: EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGG
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
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:30)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:13:27)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:13:27)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:13:30)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:13:30)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:13:30)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:13:30)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:13:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:34)
Show buried residues
Minimal score value
-3.6028
Maximal score value
0.314
Average score
-1.2185
Total score value
-131.5953
Download the table (csv)

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
278 E A -2.8895
279 Q A 0.0000
280 D A -3.1056
281 N A -2.1977
282 S A -1.4364
283 D A -2.0497
284 N A 0.0000
285 N A -1.2718
286 T A 0.0000
287 I A 0.0000
288 F A 0.0000
289 V A 0.0000
290 Q A -1.6920
291 G A -1.6405
292 L A 0.0000
293 G A -1.8663
294 E A -2.3345
295 N A -1.8035
296 V A 0.0000
297 T A -0.7405
298 I A -0.4555
299 E A -2.0449
300 S A -1.2312
301 V A 0.0000
302 A A 0.0000
303 D A -2.5116
304 Y A -0.5303
305 F A 0.0000
306 K A -2.8643
307 Q A -1.8096
308 I A -0.3060
309 G A 0.0000
310 I A 0.0000
311 I A 0.0000
312 K A -2.7337
313 T A -2.5632
314 N A 0.0000
315 K A -3.2845
316 K A -2.9207
317 T A -1.8767
318 G A -1.5529
319 Q A -1.5032
320 P A -1.6927
321 M A 0.0000
322 I A 0.0000
323 N A -0.3145
324 L A -0.2893
325 Y A -1.0707
326 T A -1.9658
327 D A -2.8594
328 R A -3.6028
329 E A -3.2887
330 T A -2.2810
331 G A -2.6636
332 K A -3.2885
333 L A 0.0000
334 K A -2.4240
335 G A -1.6067
336 E A 0.0000
337 A A 0.0000
338 T A 0.0000
339 V A 0.0000
340 S A 0.0000
341 F A 0.0000
342 D A -2.1997
343 D A -1.6996
344 P A -1.3033
345 P A -1.0449
346 S A -0.8495
347 A A 0.0000
348 K A -1.6720
349 A A -0.6528
350 A A 0.0000
351 I A -1.1345
352 D A -1.8449
353 W A -0.4503
354 F A 0.0000
355 D A -2.9214
356 G A -2.5009
357 K A -2.0544
358 E A -2.7653
359 F A -1.1108
360 S A -1.2603
361 G A -1.4684
362 N A 0.0000
363 P A -2.3830
364 I A 0.0000
365 K A -2.9355
366 V A 0.0000
367 S A -0.7987
368 F A -0.2031
369 A A 0.0000
370 T A -1.6214
371 R A -1.9666
372 R A -2.9046
373 A A -1.9375
374 D A -1.1249
375 F A 0.3140
376 N A -0.6089
377 R A -1.7165
378 G A -1.2586
379 G A -1.2005
380 G A -1.5365
381 N A -1.2440
382 G A -1.1132
383 R A -0.7333
384 G A -0.4047
385 G A -0.7208
Download PDB file
View in 3Dmol

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, -1.2185 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_9 -1.2185 View CSV PDB
model_7 -1.2358 View CSV PDB
model_2 -1.2788 View CSV PDB
model_1 -1.3654 View CSV PDB
model_10 -1.3703 View CSV PDB
model_11 -1.3731 View CSV PDB
CABS_average -1.3763 View CSV PDB
model_0 -1.3858 View CSV PDB
model_6 -1.3931 View CSV PDB
model_5 -1.4163 View CSV PDB
model_4 -1.4426 View CSV PDB
model_3 -1.4837 View CSV PDB
model_8 -1.5526 View CSV PDB
input -1.7027 View CSV PDB