Project name: tested_vpx_zn_0

Status: done

Started: 2024-12-06 17:58:52
Settings
Chain sequence(s) A: MSDPRERIPPGNSGEETIGEAFEWLNRTVEEINREAVNHLPRELIFQVWQRSWEYWHDEQGMSPSYVKYRYLCLIQKALFMHCKKGCRCLGEGHGAGGWRPGPPPPPPPGLA
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                                          (00:01:07)
[INFO]       Auto_mut: Residue number 111 from chain A and a score of 1.191 (leucine) selected for 
                       automated muatation                                                         (00:01:08)
[INFO]       Auto_mut: Residue number 18 from chain A and a score of 1.132 (isoleucine) selected   
                       for automated muatation                                                     (00:01:08)
[INFO]       Auto_mut: Residue number 69 from chain A and a score of 0.812 (tyrosine) selected for 
                       automated muatation                                                         (00:01:08)
[INFO]       Auto_mut: Residue number 90 from chain A and a score of 0.592 (leucine) selected for  
                       automated muatation                                                         (00:01:08)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.500 (methionine) selected    
                       for automated muatation                                                     (00:01:08)
[INFO]       Auto_mut: Residue number 80 from chain A and a score of 0.428 (phenylalanine)         
                       selected for automated muatation                                            (00:01:08)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into aspartic acid       (00:01:08)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into glutamic acid     (00:01:08)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into glutamic acid       (00:01:08)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into arginine            (00:01:39)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (leucine) into lysine              (00:01:39)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into lysine            (00:01:40)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into aspartic acid     (00:02:12)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into glutamic acid       (00:02:14)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into aspartic acid       (00:02:17)
[INFO]       Auto_mut: Mutating residue number 18 from chain A (isoleucine) into arginine          (00:02:43)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into arginine            (00:02:49)
[INFO]       Auto_mut: Mutating residue number 69 from chain A (tyrosine) into lysine              (00:02:50)
[INFO]       Auto_mut: Mutating residue number 90 from chain A (leucine) into glutamic acid        (00:03:18)
[INFO]       Auto_mut: Mutating residue number 90 from chain A (leucine) into aspartic acid        (00:03:28)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:03:39)
[INFO]       Auto_mut: Mutating residue number 90 from chain A (leucine) into lysine               (00:03:50)
[INFO]       Auto_mut: Mutating residue number 90 from chain A (leucine) into arginine             (00:03:59)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:04:09)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:04:27)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 80 from chain A (phenylalanine) into glutamic acid  (00:04:35)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 80 from chain A (phenylalanine) into aspartic acid  (00:04:42)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:04:58)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into lysine         (00:05:19)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (phenylalanine) into arginine       (00:05:20)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5390 kcal/mol, Difference in average score from  
                       the base case: -0.0808                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into lysine:   
                       Energy difference: 0.1673 kcal/mol, Difference in average score from the    
                       base case: -0.0774                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.7261 kcal/mol, Difference in average score from  
                       the base case: -0.0831                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (leucine) into arginine: 
                       Energy difference: 0.1304 kcal/mol, Difference in average score from the    
                       base case: -0.0844                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.9548 kcal/mol, Difference in average   
                       score from the base case: -0.1112                                           (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.1406 kcal/mol, Difference in average score from the    
                       base case: -0.1288                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -1.0749 kcal/mol, Difference in average   
                       score from the base case: -0.1089                                           (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 18 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.3723 kcal/mol, Difference in average score   
                       from the base case: -0.1234                                                 (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.3641 kcal/mol, Difference in average score from  
                       the base case: -0.0657                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.3812 kcal/mol, Difference in average score from the    
                       base case: -0.0649                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.6813 kcal/mol, Difference in average score from  
                       the base case: -0.0727                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 69 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.7384 kcal/mol, Difference in average score from the    
                       base case: -0.0798                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 90 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.2401 kcal/mol, Difference in average score from  
                       the base case: -0.0897                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 90 from chain A (leucine) into lysine:    
                       Energy difference: 0.0771 kcal/mol, Difference in average score from the    
                       base case: -0.0733                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 90 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.0584 kcal/mol, Difference in average score from  
                       the base case: -0.0888                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 90 from chain A (leucine) into arginine:  
                       Energy difference: -0.0353 kcal/mol, Difference in average score from the   
                       base case: -0.0767                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: 0.4208 kcal/mol, Difference in average score from  
                       the base case: -0.0504                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: 0.1184 kcal/mol, Difference in average score from the    
                       base case: -0.0474                                                          (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: 0.5049 kcal/mol, Difference in average score from  
                       the base case: -0.0499                                                      (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: -0.1248 kcal/mol, Difference in average score  
                       from the base case: -0.0555                                                 (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.3321 kcal/mol, Difference in average    
                       score from the base case: -0.1177                                           (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.4188 kcal/mol, Difference in average score     
                       from the base case: -0.1077                                                 (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.9333 kcal/mol, Difference in average    
                       score from the base case: -0.1134                                           (00:06:07)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (phenylalanine) into      
                       arginine: Energy difference: 0.5613 kcal/mol, Difference in average score   
                       from the base case: -0.1136                                                 (00:06:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:11)
Show buried residues
Minimal score value
-3.9319
Maximal score value
1.1911
Average score
-1.1019
Total score value
-123.4087
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 0.5000
2 S A -0.7684
3 D A -2.5605
4 P A -2.5319
5 R A -3.5906
6 E A -3.3937
7 R A -2.5735
8 I A 0.0631
9 P A -0.2886
10 P A -0.3392
11 G A -0.7799
12 N A -1.5828
13 S A -1.4267
14 G A -1.3724
15 E A -2.0266
16 E A -1.5446
17 T A -0.5357
18 I A 1.1321
19 G A -0.2116
20 E A -1.6946
21 A A -0.4327
22 F A 0.4207
23 E A -1.7152
24 W A -1.1107
25 L A 0.0000
26 N A -1.9319
27 R A -3.0054
28 T A -2.1746
29 V A 0.0000
30 E A -3.6372
31 E A -3.9319
32 I A -2.5264
33 N A -2.4929
34 R A -3.3279
35 E A -2.9354
36 A A 0.0000
37 V A -1.4016
38 N A -1.2435
39 H A -0.6297
40 L A -0.6958
41 P A -1.1424
42 R A -2.2615
43 E A -2.0372
44 L A -0.7679
45 I A 0.0000
46 F A -0.0694
47 Q A -1.5891
48 V A 0.0000
49 W A -0.7043
50 Q A -1.7552
51 R A -2.5427
52 S A 0.0000
53 W A -1.9409
54 E A -2.7763
55 Y A -1.5908
56 W A -1.5578
57 H A -2.1820
58 D A -3.4454
59 E A -3.2562
60 Q A -2.5891
61 G A -1.9668
62 M A -0.7027
63 S A -0.3278
64 P A -0.3057
65 S A 0.3181
66 Y A 0.4246
67 V A 0.0000
68 K A 0.0773
69 Y A 0.8122
70 R A 0.0329
71 Y A 0.0000
72 L A 0.0000
73 C A -0.0600
74 L A 0.1144
75 I A 0.0000
76 Q A -0.8755
77 K A -1.0481
78 A A -0.2763
79 L A -0.1002
80 F A 0.4283
81 M A -0.2794
82 H A -0.7430
83 C A -0.6024
84 K A -1.7739
85 K A -2.4048
86 G A -1.8872
87 C A -1.0969
88 R A -1.4605
89 C A -0.1039
90 L A 0.5919
91 G A -0.9569
92 E A -2.2008
93 G A -1.9038
94 H A -2.1152
95 G A -1.5956
96 A A -0.6788
97 G A -1.0895
98 G A -0.7619
99 W A -0.1667
100 R A -1.7517
101 P A -1.2111
102 G A -1.0683
103 P A -1.1671
104 P A -1.3739
105 P A -1.0073
106 P A -1.1709
107 P A -0.6223
108 P A -0.2485
109 P A -0.1803
110 G A 0.0951
111 L A 1.1911
112 A A 0.2975
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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
ID18A -1.0749 -0.1089 View CSV PDB
IE18A -0.9548 -0.1112 View CSV PDB
LR90A -0.0353 -0.0767 View CSV PDB
MR1A -0.1248 -0.0555 View CSV PDB
LD90A 0.0584 -0.0888 View CSV PDB
LR111A 0.1304 -0.0844 View CSV PDB
LK111A 0.1673 -0.0774 View CSV PDB
MK1A 0.1184 -0.0474 View CSV PDB
FE80A 0.3321 -0.1177 View CSV PDB
FK80A 0.4188 -0.1077 View CSV PDB
YE69A 0.3641 -0.0657 View CSV PDB
YK69A 0.3812 -0.0649 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018