Project name: d092b2fae0fe28d

Status: done

Started: 2026-04-24 12:09:32
Settings
Chain sequence(s) H: QVQLQQPGAELVKPGASVKMSCKASGYTFTSYNMHWVKQTPGQGLEWIGVIYSGNGDTSYNQKFKGKATLTADKSSSTAYMQINSLTSEDSAVYYCARERDTRFGNWGQGTLVTVSA
L: NIVLTQSPASLAVSLGLRATISCRASESVDIYGNSFMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQNNEDPYTFGGGTKLEIK
input PDB
Selected Chain(s) H,L
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]                                                (00:00:09)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:09)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:09)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:09)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:39)
[INFO]       Auto_mut: Residue number 34 from chain L and a score of 1.145 (tyrosine) selected for 
                       automated muatation                                                         (00:01:42)
[INFO]       Auto_mut: Residue number 123 from chain H and a score of 0.936 (leucine) selected for 
                       automated muatation                                                         (00:01:42)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 0.921 (leucine) selected for  
                       automated muatation                                                         (00:01:42)
[INFO]       Auto_mut: Residue number 3 from chain L and a score of 0.847 (valine) selected for    
                       automated muatation                                                         (00:01:42)
[INFO]       Auto_mut: Residue number 31 from chain L and a score of 0.518 (isoleucine) selected   
                       for automated muatation                                                     (00:01:42)
[INFO]       Auto_mut: Residue number 101 from chain H and a score of 0.412 (valine) selected for  
                       automated muatation                                                         (00:01:42)
[INFO]       Auto_mut: Mutating residue number 34 from chain L (tyrosine) into glutamic acid       (00:01:42)
[INFO]       Auto_mut: Mutating residue number 34 from chain L (tyrosine) into aspartic acid       (00:01:42)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into glutamic acid       (00:01:42)
[INFO]       Auto_mut: Mutating residue number 34 from chain L (tyrosine) into arginine            (00:02:38)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into lysine              (00:02:41)
[INFO]       Auto_mut: Mutating residue number 34 from chain L (tyrosine) into lysine              (00:02:42)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into aspartic acid       (00:03:43)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into glutamic acid        (00:03:50)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into aspartic acid        (00:03:54)
[INFO]       Auto_mut: Mutating residue number 123 from chain H (leucine) into arginine            (00:04:42)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into lysine               (00:04:51)
[INFO]       Auto_mut: Mutating residue number 12 from chain H (leucine) into arginine             (00:04:54)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into glutamic acid          (00:05:50)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into aspartic acid          (00:05:58)
[INFO]       Auto_mut: Mutating residue number 31 from chain L (isoleucine) into glutamic acid     (00:06:03)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into lysine                 (00:06:54)
[INFO]       Auto_mut: Mutating residue number 3 from chain L (valine) into arginine               (00:07:01)
[INFO]       Auto_mut: Mutating residue number 31 from chain L (isoleucine) into lysine            (00:07:11)
[INFO]       Auto_mut: Mutating residue number 31 from chain L (isoleucine) into aspartic acid     (00:08:28)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into glutamic acid        (00:08:32)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into aspartic acid        (00:08:38)
[INFO]       Auto_mut: Mutating residue number 31 from chain L (isoleucine) into arginine          (00:09:43)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into lysine               (00:09:49)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into arginine             (00:09:50)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain L (tyrosine) into glutamic  
                       acid: Energy difference: 0.4637 kcal/mol, Difference in average score from  
                       the base case: -0.0317                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain L (tyrosine) into lysine:   
                       Energy difference: 0.0277 kcal/mol, Difference in average score from the    
                       base case: -0.0353                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain L (tyrosine) into aspartic  
                       acid: Energy difference: 0.5506 kcal/mol, Difference in average score from  
                       the base case: -0.0316                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain L (tyrosine) into arginine: 
                       Energy difference: -0.1819 kcal/mol, Difference in average score from the   
                       base case: -0.0388                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.1406 kcal/mol, Difference in average score from  
                       the base case: -0.0487                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into lysine:   
                       Energy difference: -0.0338 kcal/mol, Difference in average score from the   
                       base case: -0.0358                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.6068 kcal/mol, Difference in average score from  
                       the base case: -0.0326                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain H (leucine) into arginine: 
                       Energy difference: 0.1024 kcal/mol, Difference in average score from the    
                       base case: -0.0422                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into glutamic   
                       acid: Energy difference: 0.6557 kcal/mol, Difference in average score from  
                       the base case: -0.0531                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into lysine:    
                       Energy difference: 0.1485 kcal/mol, Difference in average score from the    
                       base case: -0.0513                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into aspartic   
                       acid: Energy difference: 1.0681 kcal/mol, Difference in average score from  
                       the base case: -0.0583                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain H (leucine) into arginine:  
                       Energy difference: 0.2821 kcal/mol, Difference in average score from the    
                       base case: -0.0513                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into glutamic     
                       acid: Energy difference: -0.2368 kcal/mol, Difference in average score from 
                       the base case: -0.0422                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into lysine:      
                       Energy difference: -0.2610 kcal/mol, Difference in average score from the   
                       base case: -0.0516                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into aspartic     
                       acid: Energy difference: -0.3146 kcal/mol, Difference in average score from 
                       the base case: -0.0419                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain L (valine) into arginine:    
                       Energy difference: -0.5635 kcal/mol, Difference in average score from the   
                       base case: -0.0520                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain L (isoleucine) into         
                       glutamic acid: Energy difference: 0.4115 kcal/mol, Difference in average    
                       score from the base case: -0.0328                                           (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain L (isoleucine) into lysine: 
                       Energy difference: -0.0749 kcal/mol, Difference in average score from the   
                       base case: -0.0284                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain L (isoleucine) into         
                       aspartic acid: Energy difference: 0.6784 kcal/mol, Difference in average    
                       score from the base case: -0.0293                                           (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain L (isoleucine) into         
                       arginine: Energy difference: -0.8417 kcal/mol, Difference in average score  
                       from the base case: -0.0232                                                 (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into glutamic   
                       acid: Energy difference: 1.1430 kcal/mol, Difference in average score from  
                       the base case: -0.0175                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into lysine:    
                       Energy difference: 0.5256 kcal/mol, Difference in average score from the    
                       base case: -0.0186                                                          (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into aspartic   
                       acid: Energy difference: 1.3605 kcal/mol, Difference in average score from  
                       the base case: -0.0147                                                      (00:11:10)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into arginine:  
                       Energy difference: 0.7295 kcal/mol, Difference in average score from the    
                       base case: -0.0310                                                          (00:11:10)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:16)
Show buried residues
Minimal score value
-2.9724
Maximal score value
1.1453
Average score
-0.6894
Total score value
-157.1722
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
1 Q H -1.1891
2 V H -0.5377
3 Q H -1.4123
4 L H 0.0000
5 Q H -1.5849
6 Q H -1.1102
7 P H -0.8659
8 G H -0.7273
9 A H 0.1843
11 E H -0.1547
12 L H 0.9215
13 V H -0.3825
14 K H -1.6224
15 P H -1.3921
16 G H -1.1843
17 A H -0.9910
18 S H -1.0776
19 V H 0.0000
20 K H -1.3037
21 M H 0.0000
22 S H -0.6384
23 C H 0.0000
24 K H -1.4088
25 A H 0.0000
26 S H -0.8562
27 G H -0.7099
28 Y H -0.1930
29 T H -0.1249
30 F H 0.0000
35 T H -0.5965
36 S H -0.4504
37 Y H -0.5720
38 N H -0.7913
39 M H 0.0000
40 H H 0.0000
41 W H 0.0000
42 V H 0.0000
43 K H 0.0000
44 Q H -0.3895
45 T H -0.9919
46 P H -0.8872
47 G H -1.2633
48 Q H -1.7068
49 G H -1.1196
50 L H 0.0000
51 E H -0.7492
52 W H 0.0000
53 I H 0.0000
54 G H 0.0000
55 V H -0.0458
56 I H 0.0000
57 Y H -0.4242
58 S H 0.0000
59 G H -1.1834
62 N H -1.8794
63 G H -1.7968
64 D H -2.1286
65 T H -0.9137
66 S H -0.8016
67 Y H -1.2062
68 N H -1.9809
69 Q H -2.9724
70 K H -2.9078
71 F H 0.0000
72 K H -2.8640
74 G H -1.9298
75 K H -1.6852
76 A H 0.0000
77 T H -0.7168
78 L H 0.0000
79 T H -0.4793
80 A H -0.5780
81 D H -1.2272
82 K H -1.4417
83 S H -0.9023
84 S H -0.8228
85 S H -0.9237
86 T H 0.0000
87 A H 0.0000
88 Y H -0.2884
89 M H 0.0000
90 Q H -0.9065
91 I H 0.0000
92 N H -0.9562
93 S H -0.9581
94 L H 0.0000
95 T H -1.3104
96 S H -1.4522
97 E H -1.9750
98 D H 0.0000
99 S H -0.4187
100 A H 0.0000
101 V H 0.4116
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H 0.0000
107 E H -1.6215
108 R H -2.9587
109 D H -2.7445
113 T H -1.4072
114 R H 0.0000
115 F H 0.0000
116 G H -1.3418
117 N H -0.9599
118 W H -0.8660
119 G H 0.0000
120 Q H -1.7875
121 G H 0.0000
122 T H 0.0000
123 L H 0.9359
124 V H 0.0000
125 T H 0.0832
126 V H 0.0000
127 S H -0.4185
128 A H -0.4350
1 N L -1.5121
2 I L 0.0000
3 V L 0.8474
4 L L 0.0000
5 T L -0.6536
6 Q L -0.7010
7 S L -0.6443
8 P L -0.4644
9 A L -0.5466
10 S L -0.9596
11 L L -0.5076
12 A L -0.8662
13 V L 0.0000
14 S L -0.4642
15 L L -0.0026
16 G L -0.4451
17 L L -0.0386
18 R L -1.9470
19 A L 0.0000
20 T L -0.7456
21 I L 0.0000
22 S L -0.9204
23 C L 0.0000
24 R L -2.5638
25 A L 0.0000
26 S L -1.0631
27 E L -1.7957
28 S L -1.7764
29 V L 0.0000
30 D L -0.9508
31 I L 0.5177
34 Y L 1.1453
35 G L -0.0906
36 N L -0.6916
37 S L -0.7632
38 F L -0.1630
39 M L 0.0000
40 H L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L 0.0000
44 Q L -1.2157
45 K L -1.6010
46 P L -1.0823
47 G L -1.4602
48 Q L -2.0846
49 P L -1.4394
50 P L 0.0000
51 K L -1.4175
52 L L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.0944
56 L L -0.2839
57 A L 0.0000
65 S L -0.4707
66 N L -0.4581
67 L L 0.0262
68 E L -0.5175
69 S L -0.5632
70 G L -0.5701
71 V L 0.0000
72 P L -0.2817
74 A L -0.3767
75 R L -1.2846
76 F L 0.0000
77 S L -0.5570
78 G L -0.3554
79 S L -0.7527
80 G L -1.4902
83 S L -2.0439
84 R L -2.8815
85 T L -2.5487
86 D L -2.6299
87 F L 0.0000
88 T L -0.8092
89 L L 0.0000
90 T L -1.0003
91 I L 0.0000
92 D L -2.3848
93 P L -1.6282
94 V L 0.0000
95 E L -1.8260
96 A L -1.5168
97 D L -2.1331
98 D L 0.0000
99 A L -1.6568
100 A L 0.0000
101 T L -1.1164
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 Q L 0.0000
107 N L -0.5010
108 N L -0.8592
109 E L -1.3939
114 D L -1.8421
115 P L -1.6476
116 Y L -0.4652
117 T L -0.1774
118 F L 0.0000
119 G L 0.0000
120 G L -0.8407
121 G L -0.7421
122 T L 0.0000
123 K L -1.9122
124 L L 0.0000
125 E L -1.9635
126 I L -1.1372
127 K L -1.3513
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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
VR3L -0.5635 -0.052 View CSV PDB
VK3L -0.261 -0.0516 View CSV PDB
IR31L -0.8417 -0.0232 View CSV PDB
YR34L -0.1819 -0.0388 View CSV PDB
LK123H -0.0338 -0.0358 View CSV PDB
IK31L -0.0749 -0.0284 View CSV PDB
YK34L 0.0277 -0.0353 View CSV PDB
LR123H 0.1024 -0.0422 View CSV PDB
LK12H 0.1485 -0.0513 View CSV PDB
LR12H 0.2821 -0.0513 View CSV PDB
VR101H 0.7295 -0.031 View CSV PDB
VK101H 0.5256 -0.0186 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018