Project name: Structure

Status: done

Started: 2026-07-23 18:08:02
Chain sequence(s) H: QVQLQQPGAELVEPGGSVKLSCKASGYTFTSHWMHWVKQRPGQGLEWIGEINPSSGRNNYNEKFKSKATLTVDKSSSTAYMQFSSLTSEDSAVYYCVRYYGYDEAMDYWGQGTSVTVSS
L: DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSNGITYLYWYLQKPGQSPQLLIYQMSNLASGVPDRFSSSGSGTDFTLRISRVEAEDVGVYYCAQNLELPYTFGGGTKLEIK
input PDB
Selected Chain(s) H,L
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 all chain(s) selected           (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:26)
[INFO]       AutoMut:  Residue number 9 from chain L and a score of 1.535 (phenylalanine) selected 
                       for automated mutation                                                      (00:01:27)
[INFO]       AutoMut:  Residue number 117 from chain H and a score of 1.364 (tyrosine) selected    
                       for automated mutation                                                      (00:01:27)
[INFO]       AutoMut:  Residue number 3 from chain L and a score of 0.923 (valine) selected for    
                       automated mutation                                                          (00:01:27)
[INFO]       AutoMut:  Residue number 12 from chain H and a score of 0.898 (leucine) selected for  
                       automated mutation                                                          (00:01:27)
[INFO]       AutoMut:  Residue number 30 from chain L and a score of 0.814 (leucine) selected for  
                       automated mutation                                                          (00:01:27)
[INFO]       AutoMut:  Residue number 36 from chain L and a score of 0.814 (isoleucine) selected   
                       for automated mutation                                                      (00:01:27)
[INFO]       AutoMut:  Mutating residue number 9 from chain L (phenylalanine) into glutamic acid   (00:01:27)
[INFO]       AutoMut:  Mutating residue number 9 from chain L (phenylalanine) into aspartic acid   (00:01:27)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (tyrosine) into glutamic acid      (00:01:27)
[INFO]       AutoMut:  Mutating residue number 9 from chain L (phenylalanine) into arginine        (00:01:33)
[INFO]       AutoMut:  Mutating residue number 9 from chain L (phenylalanine) into lysine          (00:01:35)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (tyrosine) into lysine             (00:01:43)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (tyrosine) into aspartic acid      (00:01:44)
[INFO]       AutoMut:  Mutating residue number 3 from chain L (valine) into glutamic acid          (00:01:49)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (tyrosine) into arginine           (00:01:56)
[INFO]       AutoMut:  Mutating residue number 3 from chain L (valine) into lysine                 (00:01:57)
[INFO]       AutoMut:  Mutating residue number 3 from chain L (valine) into aspartic acid          (00:02:07)
[INFO]       AutoMut:  Mutating residue number 3 from chain L (valine) into arginine               (00:02:13)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (leucine) into glutamic acid        (00:02:16)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (leucine) into aspartic acid        (00:02:22)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (leucine) into lysine               (00:02:23)
[INFO]       AutoMut:  Mutating residue number 30 from chain L (leucine) into glutamic acid        (00:02:27)
[INFO]       AutoMut:  Mutating residue number 12 from chain H (leucine) into arginine             (00:02:28)
[INFO]       AutoMut:  Mutating residue number 30 from chain L (leucine) into lysine               (00:02:38)
[INFO]       AutoMut:  Mutating residue number 30 from chain L (leucine) into aspartic acid        (00:02:38)
[INFO]       AutoMut:  Mutating residue number 36 from chain L (isoleucine) into glutamic acid     (00:02:40)
[INFO]       AutoMut:  Mutating residue number 30 from chain L (leucine) into arginine             (00:02:45)
[INFO]       AutoMut:  Mutating residue number 36 from chain L (isoleucine) into lysine            (00:02:49)
[INFO]       AutoMut:  Mutating residue number 36 from chain L (isoleucine) into aspartic acid     (00:02:57)
[INFO]       AutoMut:  Mutating residue number 36 from chain L (isoleucine) into arginine          (00:03:06)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain L (phenylalanine) into       
                       glutamic acid: Energy difference: 0.1287 kcal/mol, Difference in average    
                       score from the base case: -0.0541                                           (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain L (phenylalanine) into       
                       lysine: Energy difference: -0.4359 kcal/mol, Difference in average score    
                       from the base case: -0.0524                                                 (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain L (phenylalanine) into       
                       aspartic acid: Energy difference: -0.2514 kcal/mol, Difference in average   
                       score from the base case: -0.0536                                           (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain L (phenylalanine) into       
                       arginine: Energy difference: 0.0655 kcal/mol, Difference in average score   
                       from the base case: -0.0544                                                 (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 0.2132 kcal/mol, Difference in average score from  
                       the base case: -0.0377                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (tyrosine) into lysine:  
                       Energy difference: 0.4245 kcal/mol, Difference in average score from the    
                       base case: -0.0363                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: -0.0936 kcal/mol, Difference in average score from 
                       the base case: -0.0314                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (tyrosine) into          
                       arginine: Energy difference: -0.9333 kcal/mol, Difference in average score  
                       from the base case: -0.0181                                                 (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 3 from chain L (valine) into glutamic     
                       acid: Energy difference: 0.3498 kcal/mol, Difference in average score from  
                       the base case: -0.0381                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 3 from chain L (valine) into lysine:      
                       Energy difference: -0.4172 kcal/mol, Difference in average score from the   
                       base case: -0.0368                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 3 from chain L (valine) into aspartic     
                       acid: Energy difference: 0.0820 kcal/mol, Difference in average score from  
                       the base case: -0.0378                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 3 from chain L (valine) into arginine:    
                       Energy difference: -0.8631 kcal/mol, Difference in average score from the   
                       base case: -0.0384                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (leucine) into glutamic   
                       acid: Energy difference: 0.7944 kcal/mol, Difference in average score from  
                       the base case: -0.0501                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (leucine) into lysine:    
                       Energy difference: 0.2432 kcal/mol, Difference in average score from the    
                       base case: -0.0477                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (leucine) into aspartic   
                       acid: Energy difference: 0.5657 kcal/mol, Difference in average score from  
                       the base case: -0.0502                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 12 from chain H (leucine) into arginine:  
                       Energy difference: 0.1113 kcal/mol, Difference in average score from the    
                       base case: -0.0497                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 30 from chain L (leucine) into glutamic   
                       acid: Energy difference: -0.2841 kcal/mol, Difference in average score from 
                       the base case: -0.0459                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 30 from chain L (leucine) into lysine:    
                       Energy difference: -0.2383 kcal/mol, Difference in average score from the   
                       base case: -0.0467                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 30 from chain L (leucine) into aspartic   
                       acid: Energy difference: 0.6040 kcal/mol, Difference in average score from  
                       the base case: -0.0420                                                      (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 30 from chain L (leucine) into arginine:  
                       Energy difference: -0.1650 kcal/mol, Difference in average score from the   
                       base case: -0.0492                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 36 from chain L (isoleucine) into         
                       glutamic acid: Energy difference: 0.4452 kcal/mol, Difference in average    
                       score from the base case: -0.0439                                           (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 36 from chain L (isoleucine) into lysine: 
                       Energy difference: -0.4377 kcal/mol, Difference in average score from the   
                       base case: -0.0382                                                          (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 36 from chain L (isoleucine) into         
                       aspartic acid: Energy difference: -0.1476 kcal/mol, Difference in average   
                       score from the base case: -0.0331                                           (00:03:21)
[INFO]       AutoMut:  Effect of mutation residue number 36 from chain L (isoleucine) into         
                       arginine: Energy difference: -0.7402 kcal/mol, Difference in average score  
                       from the base case: -0.0351                                                 (00:03:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:29)
Show buried residues
Minimal score value
-3.22
Maximal score value
1.5354
Average score
-0.5086
Total score value
-117.4914
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
1 Q H -1.0634
2 V H -0.1206
3 Q H -1.0152
4 L H 0.0000
5 Q H -1.7757
6 Q H 0.0000
7 P H -1.1011
8 G H -0.7655
9 A H -0.1454
11 E H -0.1432
12 L H 0.8979
13 V H -0.2628
14 E H -1.8194
15 P H -1.5985
16 G H -1.2401
17 G H -1.1135
18 S H -1.1884
19 V H 0.0000
20 K H -1.8816
21 L H 0.0000
22 S H -0.8509
23 C H 0.0000
24 K H -1.5122
25 A H 0.0000
26 S H -0.7326
27 G H -0.4742
28 Y H 0.5002
29 T H 0.2341
30 F H 0.0000
35 T H -0.2145
36 S H -0.1114
37 H H 0.0000
38 W H 0.0400
39 M H 0.0000
40 H H 0.0000
41 W H 0.0000
42 V H 0.0000
43 K H -0.8175
44 Q H -1.0979
45 R H -1.6508
46 P H -1.0524
47 G H -1.2162
48 Q H -1.7138
49 G H -1.2938
50 L H 0.0000
51 E H -1.5983
52 W H 0.0000
53 I H 0.0000
54 G H 0.0000
55 E H -0.6387
56 I H 0.0000
57 N H -1.1760
58 P H 0.0000
59 S H -0.8051
62 S H -1.2118
63 G H -1.6914
64 R H -2.5612
65 N H -1.7627
66 N H -1.2210
67 Y H -1.0649
68 N H 0.0000
69 E H -3.2200
70 K H -3.1951
71 F H 0.0000
72 K H -3.0046
74 S H -1.7309
75 K H -1.2975
76 A H 0.0000
77 T H -0.7283
78 L H 0.0000
79 T H -0.4209
80 V H -0.2605
81 D H -0.7789
82 K H -0.9005
83 S H -0.5888
84 S H -0.6639
85 S H -0.7616
86 T H 0.0000
87 A H 0.0000
88 Y H -0.2533
89 M H 0.0000
90 Q H -1.0993
91 F H 0.0000
92 S H -0.8712
93 S H -0.8932
94 L H 0.0000
95 T H -1.2348
96 S H -1.4110
97 E H -2.0581
98 D H 0.0000
99 S H -0.6832
100 A H 0.0000
101 V H -0.1211
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 V H 0.0000
106 R H 0.0000
107 Y H 0.5163
108 Y H 0.6504
109 G H -0.1219
110 Y H 0.5298
112 D H -0.8718
113 E H -0.2912
114 A H 0.0000
115 M H 0.4983
116 D H 0.0000
117 Y H 1.3641
118 W H 0.0000
119 G H -0.7192
120 Q H -1.7330
121 G H -0.9978
122 T H 0.0000
123 S H -0.1946
124 V H 0.0000
125 T H -0.1295
126 V H 0.0000
127 S H -0.6004
128 S H -0.7541
1 D L -1.5975
2 I L 0.0000
3 V L 0.9233
4 M L 0.0000
5 T L -0.1361
6 Q L 0.0000
7 A L 0.2646
8 A L 0.7285
9 F L 1.5354
10 S L 0.0889
11 N L -0.6534
12 P L -1.1484
13 V L 0.0000
14 T L -0.5388
15 L L 0.2050
16 G L -0.7239
17 T L -0.6668
18 S L -1.2583
19 A L 0.0000
20 S L -0.6332
21 I L 0.0000
22 S L -0.6674
23 C L 0.0000
24 R L -1.4327
25 S L 0.0000
26 S L -0.7660
27 K L -1.3004
28 S L -0.7536
29 L L 0.0000
30 L L 0.8142
31 H L -0.1753
32 S L -0.6700
34 N L -1.2311
35 G L -0.4216
36 I L 0.8141
37 T L 0.0000
38 Y L 0.3256
39 L L 0.0000
40 Y L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 L L 0.0000
44 Q L 0.0000
45 K L -1.0983
46 P L -0.7204
47 G L -1.0009
48 Q L -1.2874
49 S L -0.7736
50 P L 0.0000
51 Q L -0.3225
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.2869
56 Q L -0.1314
57 M L 0.0000
65 S L -0.7080
66 N L -1.2378
67 L L -0.6686
68 A L 0.0000
69 S L -0.4032
70 G L -0.6204
71 V L -0.5256
72 P L -1.1771
74 D L -2.1477
75 R L -2.2583
76 F L 0.0000
77 S L -1.0773
78 S L 0.0000
79 S L -0.8169
80 G L -1.0188
83 S L -0.3836
84 G L -0.4758
85 T L -1.1794
86 D L -1.7196
87 F L 0.0000
88 T L -0.7960
89 L L 0.0000
90 R L -1.2980
91 I L 0.0000
92 S L -2.0232
93 R L -2.2787
94 V L 0.0000
95 E L -1.3292
96 A L -1.0134
97 E L -1.9306
98 D L -1.1551
99 V L -0.6812
100 G L 0.0000
101 V L -0.0070
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 A L 0.0000
106 Q L 0.0000
107 N L 0.1032
108 L L 0.1626
109 E L -0.5347
114 L L 0.5662
115 P L -0.3026
116 Y L 0.0000
117 T L -0.0389
118 F L 0.0000
119 G L 0.0000
120 G L -0.4040
121 G L 0.0000
122 T L 0.0000
123 K L -0.6339
124 L L 0.0000
125 E L -1.4186
126 I L -0.8084
127 K L -1.4927
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

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
VR3L -0.8631 -0.0384 View CSV PDB
FK9L -0.4359 -0.0524 View CSV PDB
IR36L -0.7402 -0.0351 View CSV PDB
FD9L -0.2514 -0.0536 View CSV PDB
LE30L -0.2841 -0.0459 View CSV PDB
IK36L -0.4377 -0.0382 View CSV PDB
LK30L -0.2383 -0.0467 View CSV PDB
VK3L -0.4172 -0.0368 View CSV PDB
YR117H -0.9333 -0.0181 View CSV PDB
YD117H -0.0936 -0.0314 View CSV PDB
LR12H 0.1113 -0.0497 View CSV PDB
LK12H 0.2432 -0.0477 View CSV PDB