Project name: sbinder1

Status: done

Started: 2025-02-05 20:01:17
Settings
Chain sequence(s) A: VEEIKKAAKEAEAALDALAKADPSLAAGMAKAKAVVKRYEELGIEYAKTSKVAAKGALTKIKLLLDAAKAELAKVKAA
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                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:15)
[INFO]       Auto_mut: Residue number 52 from chain A and a score of 0.331 (valine) selected for   
                       automated muatation                                                         (00:02:16)
[INFO]       Auto_mut: Residue number 63 from chain A and a score of 0.155 (leucine) selected for  
                       automated muatation                                                         (00:02:16)
[INFO]       Auto_mut: Residue number 25 from chain A and a score of -0.154 (leucine) selected for 
                       automated muatation                                                         (00:02:16)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (valine) into glutamic acid         (00:02:16)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (valine) into lysine                (00:02:16)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (valine) into aspartic acid         (00:02:16)
[INFO]       Auto_mut: Mutating residue number 52 from chain A (valine) into arginine              (00:03:29)
[INFO]       Auto_mut: Mutating residue number 63 from chain A (leucine) into glutamic acid        (00:03:31)
[INFO]       Auto_mut: Mutating residue number 63 from chain A (leucine) into lysine               (00:03:45)
[INFO]       Auto_mut: Mutating residue number 63 from chain A (leucine) into aspartic acid        (00:04:53)
[INFO]       Auto_mut: Mutating residue number 63 from chain A (leucine) into arginine             (00:04:55)
[INFO]       Auto_mut: Mutating residue number 25 from chain A (leucine) into glutamic acid        (00:05:09)
[INFO]       Auto_mut: Mutating residue number 25 from chain A (leucine) into lysine               (00:06:07)
[INFO]       Auto_mut: Mutating residue number 25 from chain A (leucine) into aspartic acid        (00:06:13)
[INFO]       Auto_mut: Mutating residue number 25 from chain A (leucine) into arginine             (00:06:28)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (valine) into glutamic    
                       acid: Energy difference: -1.1119 kcal/mol, Difference in average score from 
                       the base case: -0.1648                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (valine) into lysine:     
                       Energy difference: -0.2035 kcal/mol, Difference in average score from the   
                       base case: -0.1347                                                          (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.9508 kcal/mol, Difference in average score from 
                       the base case: -0.1630                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain A (valine) into arginine:   
                       Energy difference: -0.1596 kcal/mol, Difference in average score from the   
                       base case: -0.1656                                                          (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 63 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.4410 kcal/mol, Difference in average score from  
                       the base case: -0.1683                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 63 from chain A (leucine) into lysine:    
                       Energy difference: 0.2233 kcal/mol, Difference in average score from the    
                       base case: -0.1445                                                          (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 63 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.8821 kcal/mol, Difference in average score from  
                       the base case: -0.1711                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 63 from chain A (leucine) into arginine:  
                       Energy difference: 0.3783 kcal/mol, Difference in average score from the    
                       base case: -0.1771                                                          (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 25 from chain A (leucine) into glutamic   
                       acid: Energy difference: 1.8099 kcal/mol, Difference in average score from  
                       the base case: -0.0730                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 25 from chain A (leucine) into lysine:    
                       Energy difference: 0.4365 kcal/mol, Difference in average score from the    
                       base case: -0.0184                                                          (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 25 from chain A (leucine) into aspartic   
                       acid: Energy difference: 1.6276 kcal/mol, Difference in average score from  
                       the base case: -0.0771                                                      (00:07:48)
[INFO]       Auto_mut: Effect of mutation residue number 25 from chain A (leucine) into arginine:  
                       Energy difference: 0.2602 kcal/mol, Difference in average score from the    
                       base case: -0.0790                                                          (00:07:48)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:49)
Show buried residues
Minimal score value
-4.2926
Maximal score value
0.3307
Average score
-1.4287
Total score value
-111.4385
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 V A -2.0249
2 E A -3.1417
3 E A -3.6487
4 I A 0.0000
5 K A -3.7526
6 K A -4.2926
7 A A 0.0000
8 A A 0.0000
9 K A -4.0814
10 E A -3.7166
11 A A 0.0000
12 E A -2.6574
13 A A -1.9473
14 A A -2.0621
15 L A 0.0000
16 D A -1.7942
17 A A -1.2977
18 L A 0.0000
19 A A -1.1897
20 K A -2.0415
21 A A -1.3847
22 D A -1.2183
23 P A -0.8975
24 S A -0.4774
25 L A -0.1545
26 A A -0.7166
27 A A -0.4018
28 G A -0.7610
29 M A -0.9502
30 A A -0.9726
31 K A -1.7791
32 A A -1.1706
33 K A -1.7119
34 A A -1.3960
35 V A -1.1117
36 V A 0.0000
37 K A -3.1479
38 R A -2.6322
39 Y A -1.7683
40 E A -2.5079
41 E A -2.8123
42 L A -1.7185
43 G A 0.0000
44 I A -1.7482
45 E A -2.1838
46 Y A -1.3516
47 A A -1.5812
48 K A -2.2327
49 T A -1.2238
50 S A -1.0926
51 K A -1.5264
52 V A 0.3307
53 A A -0.4749
54 A A 0.0000
55 K A -1.7903
56 G A -1.0569
57 A A 0.0000
58 L A -1.1041
59 T A -0.7697
60 K A -0.7339
61 I A 0.0000
62 K A -1.2669
63 L A 0.1550
64 L A -0.2984
65 L A -1.8209
66 D A -2.0993
67 A A -1.1515
68 A A 0.0000
69 K A -2.2455
70 A A -1.9054
71 E A -2.3754
72 L A -2.0682
73 A A -1.8299
74 K A -2.5498
75 V A -1.7765
76 K A -2.1923
77 A A -1.3450
78 A A -0.7897
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
VE52A -1.1119 -0.1648 View CSV PDB
VD52A -0.9508 -0.163 View CSV PDB
LK63A 0.2233 -0.1445 View CSV PDB
LR63A 0.3783 -0.1771 View CSV PDB
LR25A 0.2602 -0.079 View CSV PDB
LD25A 1.6276 -0.0771 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018