Project name: test

Status: done

Started: 2025-11-10 08:10:27
Settings
Chain sequence(s) A: MVKVKFKYKGEEKEVDTSKIKKVWRVGKMVSFTYDDNGKTGRGAVSEKDAPKELLDMLARAEREKK
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                                          (00:03:12)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.572 omitted from automated   
                       muatation (excluded by the user).                                           (00:03:13)
[INFO]       Auto_mut: Residue number 26 from chain A and a score of 0.566 (valine) selected for   
                       automated muatation                                                         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (valine) into glutamic acid         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (valine) into lysine                (00:03:13)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (valine) into aspartic acid         (00:03:13)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (valine) into arginine              (00:05:04)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.9929 kcal/mol, Difference in average score from 
                       the base case: -0.0654                                                      (00:07:05)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (valine) into lysine:     
                       Energy difference: 0.0829 kcal/mol, Difference in average score from the    
                       base case: -0.0761                                                          (00:07:05)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.2194 kcal/mol, Difference in average score from 
                       the base case: -0.0579                                                      (00:07:05)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (valine) into arginine:   
                       Energy difference: -0.1273 kcal/mol, Difference in average score from the   
                       base case: -0.0713                                                          (00:07:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:06)
Show buried residues
Minimal score value
-5.1011
Maximal score value
0.5717
Average score
-2.0629
Total score value
-136.1492
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 M A 0.5717
2 V A -0.9242
3 K A -2.8248
4 V A 0.0000
5 K A -4.0747
6 F A 0.0000
7 K A -4.0058
8 Y A -2.8684
9 K A -2.9478
10 G A -2.9688
11 E A -3.9636
12 E A -4.5800
13 K A -4.1173
14 E A -4.0580
15 V A 0.0000
16 D A -2.2955
17 T A -1.6481
18 S A -1.6250
19 K A -3.1038
20 I A 0.0000
21 K A -3.1144
22 K A -2.6545
23 V A 0.0000
24 W A -0.6582
25 R A -0.6771
26 V A 0.5663
27 G A -0.6692
28 K A -1.8616
29 M A -0.7019
30 V A 0.0000
31 S A 0.0000
32 F A 0.0000
33 T A 0.0000
34 Y A 0.0000
35 D A -3.6005
36 D A -2.8889
37 N A -2.7181
38 G A -2.3857
39 K A -2.9922
40 T A -2.3785
41 G A 0.0000
42 R A -2.4870
43 G A 0.0000
44 A A -0.8051
45 V A 0.0000
46 S A -1.6896
47 E A -2.3271
48 K A -3.1261
49 D A -3.1474
50 A A -2.4663
51 P A -2.5324
52 K A -2.9894
53 E A -2.4472
54 L A 0.0000
55 L A -2.0244
56 D A -3.0661
57 M A -2.5269
58 L A 0.0000
59 A A -2.8530
60 R A -3.7479
61 A A -3.8664
62 E A -4.3392
63 R A -4.8770
64 E A -5.1011
65 K A -4.1731
66 K A -3.3879
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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
VE26A -0.9929 -0.0654 View CSV PDB
VR26A -0.1273 -0.0713 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018