Project name: 3794722dde09413

Status: done

Started: 2026-04-08 10:09:48
Settings
Chain sequence(s) A: GKVPTIVMVDAYKRYK
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:00:05)
[INFO]       Auto_mut: Residue number 8 from chain A and a score of 3.662 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 7 from chain A and a score of 3.029 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 9 from chain A and a score of 2.848 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 10 from chain A and a score of 1.819 omitted from automated  
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 1.451 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 4 from chain A and a score of 0.689 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 0.647 omitted from automated   
                       muatation (excluded by the user).                                           (00:00:06)
[INFO]       Auto_mut: Residue number 12 from chain A and a score of -0.159 (alanine) selected for 
                       automated muatation                                                         (00:00:06)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (alanine) into glutamic acid        (00:00:06)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (alanine) into lysine               (00:00:06)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (alanine) into aspartic acid        (00:00:06)
[INFO]       Auto_mut: Mutating residue number 12 from chain A (alanine) into arginine             (00:00:15)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (alanine) into glutamic   
                       acid: Energy difference: -0.0725 kcal/mol, Difference in average score from 
                       the base case: -0.2853                                                      (00:00:25)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (alanine) into lysine:    
                       Energy difference: -0.5121 kcal/mol, Difference in average score from the   
                       base case: -0.2671                                                          (00:00:25)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (alanine) into aspartic   
                       acid: Energy difference: 0.0981 kcal/mol, Difference in average score from  
                       the base case: -0.2807                                                      (00:00:25)
[INFO]       Auto_mut: Effect of mutation residue number 12 from chain A (alanine) into arginine:  
                       Energy difference: -0.8009 kcal/mol, Difference in average score from the   
                       base case: -0.2890                                                          (00:00:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:25)
Show buried residues
Minimal score value
-2.1193
Maximal score value
3.6615
Average score
0.3281
Total score value
5.2493
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
2 G A -0.9078
3 K A -1.1215
4 V A 0.6894
5 P A 0.6475
6 T A 1.4510
7 I A 3.0289
8 V A 3.6615
9 M A 2.8484
10 V A 1.8191
11 D A -0.3600
12 A A -0.1591
13 Y A -0.3032
14 K A -1.6539
15 R A -2.1193
16 Y A -0.8079
17 K A -1.4638
Download PDB file
View in 3Dmol
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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
AR12A -0.8009 -0.289 View CSV PDB
AK12A -0.5121 -0.2671 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018