Project name: inpp5k SKICH

Status: done

Started: 2025-12-12 15:17:40
Settings
Chain sequence(s) A: SAPLIVLMPEDLWTVENDMMVSYSSTSDFPSSPWDWIGLYKVGLRDVNDYVSYAWVGDSKVSCSDNLNQVYIDISNIPTTEDEFLLCYYSNSLRSVVGISRPFQIPPGSLREDPLGEAQPQI
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
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 minimalization                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:35)
[INFO]       Auto_mut: Residue number 425 from chain A and a score of 1.934 (isoleucine) selected  
                       for automated muatation                                                     (00:01:37)
[INFO]       Auto_mut: Residue number 332 from chain A and a score of 1.538 (valine) selected for  
                       automated muatation                                                         (00:01:37)
[INFO]       Auto_mut: Residue number 448 from chain A and a score of 1.198 (isoleucine) selected  
                       for automated muatation                                                     (00:01:37)
[INFO]       Auto_mut: Residue number 422 from chain A and a score of 0.787 (valine) selected for  
                       automated muatation                                                         (00:01:37)
[INFO]       Auto_mut: Residue number 360 from chain A and a score of 0.749 (tryptophan) selected  
                       for automated muatation                                                     (00:01:37)
[INFO]       Auto_mut: Residue number 329 from chain A and a score of 0.674 (proline) selected for 
                       automated muatation                                                         (00:01:37)
[INFO]       Auto_mut: Mutating residue number 425 from chain A (isoleucine) into glutamic acid    (00:01:37)
[INFO]       Auto_mut: Mutating residue number 425 from chain A (isoleucine) into aspartic acid    (00:01:37)
[INFO]       Auto_mut: Mutating residue number 332 from chain A (valine) into glutamic acid        (00:01:37)
[INFO]       Auto_mut: Mutating residue number 425 from chain A (isoleucine) into arginine         (00:02:27)
[INFO]       Auto_mut: Mutating residue number 332 from chain A (valine) into lysine               (00:02:29)
[INFO]       Auto_mut: Mutating residue number 425 from chain A (isoleucine) into lysine           (00:02:41)
[INFO]       Auto_mut: Mutating residue number 332 from chain A (valine) into aspartic acid        (00:03:28)
[INFO]       Auto_mut: Mutating residue number 448 from chain A (isoleucine) into glutamic acid    (00:03:50)
[INFO]       Auto_mut: Mutating residue number 448 from chain A (isoleucine) into aspartic acid    (00:04:14)
[INFO]       Auto_mut: Mutating residue number 332 from chain A (valine) into arginine             (00:04:21)
[INFO]       Auto_mut: Mutating residue number 448 from chain A (isoleucine) into lysine           (00:04:42)
[INFO]       Auto_mut: Mutating residue number 448 from chain A (isoleucine) into arginine         (00:05:02)
[INFO]       Auto_mut: Mutating residue number 422 from chain A (valine) into glutamic acid        (00:05:24)
[INFO]       Auto_mut: Mutating residue number 422 from chain A (valine) into aspartic acid        (00:05:37)
[INFO]       Auto_mut: Mutating residue number 360 from chain A (tryptophan) into glutamic acid    (00:06:03)
[INFO]       Auto_mut: Mutating residue number 422 from chain A (valine) into lysine               (00:06:28)
[INFO]       Auto_mut: Mutating residue number 422 from chain A (valine) into arginine             (00:06:28)
[INFO]       Auto_mut: Mutating residue number 360 from chain A (tryptophan) into lysine           (00:07:18)
[INFO]       Auto_mut: Mutating residue number 360 from chain A (tryptophan) into aspartic acid    (00:07:19)
[INFO]       Auto_mut: Mutating residue number 329 from chain A (proline) into glutamic acid       (00:07:34)
[INFO]       Auto_mut: Mutating residue number 360 from chain A (tryptophan) into arginine         (00:08:07)
[INFO]       Auto_mut: Mutating residue number 329 from chain A (proline) into aspartic acid       (00:08:19)
[INFO]       Auto_mut: Mutating residue number 329 from chain A (proline) into lysine              (00:08:27)
[INFO]       Auto_mut: Mutating residue number 329 from chain A (proline) into arginine            (00:09:08)
[INFO]       Auto_mut: Effect of mutation residue number 425 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.1980 kcal/mol, Difference in average    
                       score from the base case: -0.0783                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 425 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.3033 kcal/mol, Difference in average score     
                       from the base case: -0.0721                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 425 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.0827 kcal/mol, Difference in average    
                       score from the base case: -0.0547                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 425 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.3465 kcal/mol, Difference in average score   
                       from the base case: -0.0869                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 332 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.4067 kcal/mol, Difference in average score from  
                       the base case: -0.0379                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 332 from chain A (valine) into lysine:    
                       Energy difference: 0.2504 kcal/mol, Difference in average score from the    
                       base case: -0.0453                                                          (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 332 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.6801 kcal/mol, Difference in average score from  
                       the base case: -0.0484                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 332 from chain A (valine) into arginine:  
                       Energy difference: 0.3397 kcal/mol, Difference in average score from the    
                       base case: -0.0188                                                          (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 448 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.0321 kcal/mol, Difference in average   
                       score from the base case: -0.0404                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 448 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.0452 kcal/mol, Difference in average score    
                       from the base case: -0.0385                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 448 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.0187 kcal/mol, Difference in average   
                       score from the base case: -0.0399                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 448 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.0220 kcal/mol, Difference in average score   
                       from the base case: -0.0407                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 422 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.8149 kcal/mol, Difference in average score from  
                       the base case: -0.0258                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 422 from chain A (valine) into lysine:    
                       Energy difference: 0.6715 kcal/mol, Difference in average score from the    
                       base case: -0.0387                                                          (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 422 from chain A (valine) into aspartic   
                       acid: Energy difference: 1.7367 kcal/mol, Difference in average score from  
                       the base case: -0.0428                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 422 from chain A (valine) into arginine:  
                       Energy difference: 0.6001 kcal/mol, Difference in average score from the    
                       base case: -0.0422                                                          (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 360 from chain A (tryptophan) into        
                       glutamic acid: Energy difference: -0.7674 kcal/mol, Difference in average   
                       score from the base case: -0.0524                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 360 from chain A (tryptophan) into        
                       lysine: Energy difference: -0.7237 kcal/mol, Difference in average score    
                       from the base case: -0.0606                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 360 from chain A (tryptophan) into        
                       aspartic acid: Energy difference: -0.3398 kcal/mol, Difference in average   
                       score from the base case: -0.0385                                           (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 360 from chain A (tryptophan) into        
                       arginine: Energy difference: -2.2474 kcal/mol, Difference in average score  
                       from the base case: -0.0659                                                 (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 329 from chain A (proline) into glutamic  
                       acid: Energy difference: 0.4372 kcal/mol, Difference in average score from  
                       the base case: -0.0286                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 329 from chain A (proline) into lysine:   
                       Energy difference: 0.7077 kcal/mol, Difference in average score from the    
                       base case: -0.0302                                                          (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 329 from chain A (proline) into aspartic  
                       acid: Energy difference: 0.8047 kcal/mol, Difference in average score from  
                       the base case: -0.0146                                                      (00:10:18)
[INFO]       Auto_mut: Effect of mutation residue number 329 from chain A (proline) into arginine: 
                       Energy difference: 0.2217 kcal/mol, Difference in average score from the    
                       base case: -0.0428                                                          (00:10:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:28)
Show buried residues
Minimal score value
-3.1824
Maximal score value
1.9343
Average score
-0.7395
Total score value
-90.2129
Download the table (csv)

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
327 S A -0.1566
328 A A 0.1420
329 P A 0.6737
330 L A 0.5796
331 I A 0.0000
332 V A 1.5381
333 L A 0.0000
334 M A -0.6111
335 P A -1.3892
336 E A -2.7062
337 D A -2.3658
338 L A -0.9902
339 W A -0.1638
340 T A 0.0000
341 V A -1.4983
342 E A -2.8829
343 N A -3.1824
344 D A -2.3562
345 M A 0.0000
346 M A -0.0867
347 V A 0.0000
348 S A 0.0000
349 Y A 0.0000
350 S A -0.1036
351 S A -0.2538
352 T A -0.5887
353 S A -1.1927
354 D A -1.7867
355 F A -0.6676
356 P A -0.5324
357 S A -0.4076
358 S A 0.1185
359 P A -0.2434
360 W A 0.7493
361 D A 0.0000
362 W A 0.4277
363 I A 0.0000
364 G A 0.0000
365 L A 0.0000
366 Y A 0.0000
367 K A -0.9647
368 V A -0.2392
369 G A -0.8515
370 L A -1.0509
371 R A -2.6005
372 D A -2.6089
373 V A -1.2171
374 N A -1.7178
375 D A -1.5185
376 Y A 0.0533
377 V A 0.5244
378 S A 0.0034
379 Y A 0.5175
380 A A 0.0000
381 W A -0.0676
382 V A 0.0000
383 G A -1.2553
384 D A -1.9208
385 S A -1.0686
386 K A -0.9810
387 V A 0.5361
388 S A 0.3792
389 C A 0.0119
390 S A -1.0099
391 D A -2.1888
392 N A -1.8625
393 L A -0.5508
394 N A 0.0000
395 Q A 0.0919
396 V A 0.0000
397 Y A -0.4019
398 I A 0.0000
399 D A -2.4309
400 I A -1.6861
401 S A -2.1612
402 N A -1.6216
403 I A -0.6786
404 P A -0.7384
405 T A -0.9145
406 T A -1.5332
407 E A -2.7098
408 D A -2.4066
409 E A -2.6538
410 F A 0.0000
411 L A -0.2061
412 L A 0.0000
413 C A 0.0000
414 Y A 0.0000
415 Y A 0.5463
416 S A 0.0000
417 N A -0.3698
418 S A -0.3766
419 L A -0.2417
420 R A -1.5257
421 S A -0.4838
422 V A 0.7871
423 V A 0.0000
424 G A 0.0000
425 I A 1.9343
426 S A 0.0000
427 R A -1.7483
428 P A -1.2857
429 F A 0.0000
430 Q A -2.2941
431 I A -0.9199
432 P A -0.5454
433 P A -0.5300
434 G A -1.1003
435 S A -0.8871
436 L A -0.7355
437 R A -3.0088
438 E A -3.1199
439 D A -3.0375
440 P A -1.5704
441 L A -0.2106
442 G A -1.5494
443 E A -2.2580
444 A A -1.4890
445 Q A -1.9847
446 P A -1.1030
447 Q A -0.6666
448 I A 1.1976
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Automated mutations analysis

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file.

Mutant
Energetic effect
Score comparison
WR360A -2.2474 -0.0659 View CSV PDB
WK360A -0.7237 -0.0606 View CSV PDB
IE448A -0.0321 -0.0404 View CSV PDB
IK448A -0.0452 -0.0385 View CSV PDB
IR425A 0.3465 -0.0869 View CSV PDB
IK425A 0.3033 -0.0721 View CSV PDB
PR329A 0.2217 -0.0428 View CSV PDB
VK332A 0.2504 -0.0453 View CSV PDB
VE332A 0.4067 -0.0379 View CSV PDB
VR422A 0.6001 -0.0422 View CSV PDB
PE329A 0.4372 -0.0286 View CSV PDB
VK422A 0.6715 -0.0387 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018