Project name: e56cd49dc77f5ad

Status: done

Started: 2026-02-24 20:40:39
Settings
Chain sequence(s) H: EVQLVESGGGEVQPGGSLKLSCVASGTDFSINFVRWYRQRPGKQREWVAGFTANGDTNYPDSMKGRFTISRDNAKNTVYLQINSLKSEDTAVYYCYMLDNWGQGTQVTVSS
input PDB
Selected Chain(s) H
Distance of aggregation 5 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 H 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                                          (00:00:44)
[INFO]       Auto_mut: Residue number 5 from chain H and a score of 1.058 (valine) selected for    
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Residue number 24 from chain H and a score of 0.934 (valine) selected for   
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Residue number 107 from chain H and a score of 0.611 (leucine) selected for 
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Residue number 101 from chain H and a score of 0.497 (valine) selected for  
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Residue number 36 from chain H and a score of 0.479 (isoleucine) selected   
                       for automated muatation                                                     (00:00:45)
[INFO]       Auto_mut: Residue number 88 from chain H and a score of 0.374 (tyrosine) selected for 
                       automated muatation                                                         (00:00:45)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into glutamic acid          (00:00:45)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into aspartic acid          (00:00:45)
[INFO]       Auto_mut: Mutating residue number 24 from chain H (valine) into glutamic acid         (00:00:45)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into lysine                 (00:01:21)
[INFO]       Auto_mut: Mutating residue number 5 from chain H (valine) into arginine               (00:01:22)
[INFO]       Auto_mut: Mutating residue number 24 from chain H (valine) into lysine                (00:01:24)
[INFO]       Auto_mut: Mutating residue number 24 from chain H (valine) into aspartic acid         (00:02:11)
[INFO]       Auto_mut: Mutating residue number 107 from chain H (leucine) into glutamic acid       (00:02:18)
[INFO]       Auto_mut: Mutating residue number 107 from chain H (leucine) into aspartic acid       (00:02:33)
[INFO]       Auto_mut: Mutating residue number 24 from chain H (valine) into arginine              (00:02:45)
[INFO]       Auto_mut: Mutating residue number 107 from chain H (leucine) into lysine              (00:03:02)
[INFO]       Auto_mut: Mutating residue number 107 from chain H (leucine) into arginine            (00:03:11)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into glutamic acid        (00:03:51)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into aspartic acid        (00:03:55)
[INFO]       Auto_mut: Mutating residue number 36 from chain H (isoleucine) into glutamic acid     (00:04:23)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into arginine             (00:04:27)
[INFO]       Auto_mut: Mutating residue number 101 from chain H (valine) into lysine               (00:04:28)
[INFO]       Auto_mut: Mutating residue number 36 from chain H (isoleucine) into lysine            (00:04:59)
[INFO]       Auto_mut: Mutating residue number 36 from chain H (isoleucine) into aspartic acid     (00:05:07)
[INFO]       Auto_mut: Mutating residue number 88 from chain H (tyrosine) into glutamic acid       (00:05:25)
[INFO]       Auto_mut: Mutating residue number 36 from chain H (isoleucine) into arginine          (00:05:42)
[INFO]       Auto_mut: Mutating residue number 88 from chain H (tyrosine) into aspartic acid       (00:06:00)
[INFO]       Auto_mut: Mutating residue number 88 from chain H (tyrosine) into lysine              (00:06:23)
[INFO]       Auto_mut: Mutating residue number 88 from chain H (tyrosine) into arginine            (00:06:51)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into glutamic     
                       acid: Energy difference: 0.7233 kcal/mol, Difference in average score from  
                       the base case: -0.0283                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into lysine:      
                       Energy difference: -0.5633 kcal/mol, Difference in average score from the   
                       base case: -0.0215                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into aspartic     
                       acid: Energy difference: 1.1270 kcal/mol, Difference in average score from  
                       the base case: -0.0241                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain H (valine) into arginine:    
                       Energy difference: -0.6891 kcal/mol, Difference in average score from the   
                       base case: -0.0222                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain H (valine) into glutamic    
                       acid: Energy difference: 0.8046 kcal/mol, Difference in average score from  
                       the base case: -0.0353                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain H (valine) into lysine:     
                       Energy difference: -0.2178 kcal/mol, Difference in average score from the   
                       base case: -0.0187                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain H (valine) into aspartic    
                       acid: Energy difference: 1.8534 kcal/mol, Difference in average score from  
                       the base case: -0.0170                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 24 from chain H (valine) into arginine:   
                       Energy difference: -0.2253 kcal/mol, Difference in average score from the   
                       base case: -0.0221                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain H (leucine) into glutamic  
                       acid: Energy difference: -0.1436 kcal/mol, Difference in average score from 
                       the base case: -0.0256                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain H (leucine) into lysine:   
                       Energy difference: 0.0296 kcal/mol, Difference in average score from the    
                       base case: -0.0296                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.1867 kcal/mol, Difference in average score from  
                       the base case: -0.0254                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 107 from chain H (leucine) into arginine: 
                       Energy difference: -0.0684 kcal/mol, Difference in average score from the   
                       base case: -0.0253                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into glutamic   
                       acid: Energy difference: 0.7095 kcal/mol, Difference in average score from  
                       the base case: -0.0204                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into lysine:    
                       Energy difference: -0.0576 kcal/mol, Difference in average score from the   
                       base case: -0.0171                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into aspartic   
                       acid: Energy difference: 1.2901 kcal/mol, Difference in average score from  
                       the base case: -0.0155                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 101 from chain H (valine) into arginine:  
                       Energy difference: -0.0010 kcal/mol, Difference in average score from the   
                       base case: -0.0244                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: 1.2750 kcal/mol, Difference in average    
                       score from the base case: -0.0267                                           (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain H (isoleucine) into lysine: 
                       Energy difference: 0.4714 kcal/mol, Difference in average score from the    
                       base case: -0.0198                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: 1.3737 kcal/mol, Difference in average    
                       score from the base case: -0.0199                                           (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 36 from chain H (isoleucine) into         
                       arginine: Energy difference: 0.3660 kcal/mol, Difference in average score   
                       from the base case: -0.0255                                                 (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: 2.5878 kcal/mol, Difference in average score from  
                       the base case: -0.0158                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain H (tyrosine) into lysine:   
                       Energy difference: 2.0503 kcal/mol, Difference in average score from the    
                       base case: -0.0128                                                          (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: 3.6987 kcal/mol, Difference in average score from  
                       the base case: -0.0145                                                      (00:07:47)
[INFO]       Auto_mut: Effect of mutation residue number 88 from chain H (tyrosine) into arginine: 
                       Energy difference: 1.4894 kcal/mol, Difference in average score from the    
                       base case: -0.0115                                                          (00:07:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:52)
Show buried residues
Minimal score value
-2.0225
Maximal score value
1.0585
Average score
-0.4089
Total score value
-45.3837
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 E H -1.7807
2 V H -0.3262
3 Q H -1.1593
4 L H 0.0000
5 V H 1.0585
6 E H -0.0618
7 S H -0.3190
8 G H -0.4544
9 G H -0.3625
11 G H -0.6569
12 E H -1.8372
13 V H -0.3366
14 Q H -1.1834
15 P H -0.6336
16 G H -0.5386
17 G H -0.3072
18 S H -0.2649
19 L H 0.0441
20 K H -1.3384
21 L H 0.0000
22 S H 0.0202
23 C H 0.0000
24 V H 0.9340
25 A H 0.0000
26 S H -0.1465
27 G H -0.4823
28 T H -0.4262
29 D H -1.7942
30 F H 0.0000
35 S H -0.0755
36 I H 0.4791
37 N H -1.0547
38 F H 0.1704
39 V H 0.0000
40 R H -0.2057
41 W H 0.0000
42 Y H 0.2397
43 R H 0.0000
44 Q H -0.5609
45 R H -0.5787
46 P H -0.4208
47 G H -0.8110
48 K H -1.9995
49 Q H -1.6267
50 R H -0.9901
51 E H -0.3433
52 W H 0.2980
53 V H 0.0000
54 A H 0.0000
55 G H 0.0000
56 F H 0.2191
57 T H 0.0889
58 A H -0.3361
59 N H -1.3146
63 G H -0.8102
64 D H -1.8422
65 T H -0.4622
66 N H -0.7485
67 Y H 0.0556
68 P H -0.3598
69 D H -2.0225
70 S H -0.5291
71 M H 0.0000
72 K H -1.9205
74 G H -0.8410
75 R H -0.6113
76 F H 0.0000
77 T H -0.0259
78 I H 0.0000
79 S H -0.1635
80 R H -0.2817
81 D H -0.6067
82 N H -1.3548
83 A H -0.4684
84 K H -1.7310
85 N H -0.7019
86 T H 0.0000
87 V H 0.0000
88 Y H 0.3741
89 L H 0.0000
90 Q H -0.6447
91 I H 0.0000
92 N H -0.6866
93 S H -0.3380
94 L H 0.0000
95 K H -1.5613
96 S H -0.6638
97 E H -1.8320
98 D H 0.0000
99 T H -0.0139
100 A H 0.0000
101 V H 0.4967
102 Y H 0.0000
103 Y H 0.1244
104 C H 0.0000
105 Y H 0.1999
106 M H 0.0000
107 L H 0.6108
116 D H -1.6915
117 N H -0.6310
118 W H 0.3210
119 G H 0.0000
120 Q H -1.2237
121 G H -0.3406
122 T H -0.1447
123 Q H -0.5304
124 V H 0.0000
125 T H -0.2437
126 V H 0.0000
127 S H -0.1333
128 S H -0.2303
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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
VR5H -0.6891 -0.0222 View CSV PDB
VK5H -0.5633 -0.0215 View CSV PDB
LE107H -0.1436 -0.0256 View CSV PDB
VR24H -0.2253 -0.0221 View CSV PDB
LR107H -0.0684 -0.0253 View CSV PDB
VK24H -0.2178 -0.0187 View CSV PDB
VR101H -0.001 -0.0244 View CSV PDB
VK101H -0.0576 -0.0171 View CSV PDB
IR36H 0.366 -0.0255 View CSV PDB
IK36H 0.4714 -0.0198 View CSV PDB
YR88H 1.4894 -0.0115 View CSV PDB
YK88H 2.0503 -0.0128 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018