Project name: model

Status: done

Started: 2024-06-19 14:38:24
Settings
Chain sequence(s) A: VGSLNCIVAVSQNMMGIGKNGDLPWPPPLRNEFRYFQRRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEEKGIKYKFEVYEKND
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                                          (00:02:34)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.701 (valine) selected for    
                       automated muatation                                                         (00:02:35)
[INFO]       Auto_mut: Residue number 166 from chain A and a score of 0.567 (leucine) selected for 
                       automated muatation                                                         (00:02:35)
[INFO]       Auto_mut: Residue number 147 from chain A and a score of 0.550 (phenylalanine)        
                       selected for automated muatation                                            (00:02:35)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.531 (glycine) selected for   
                       automated muatation                                                         (00:02:35)
[INFO]       Auto_mut: Residue number 115 from chain A and a score of 0.207 (valine) selected for  
                       automated muatation                                                         (00:02:35)
[INFO]       Auto_mut: Residue number 111 from chain A and a score of 0.110 (methionine) selected  
                       for automated muatation                                                     (00:02:35)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (valine) into glutamic acid          (00:02:35)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (valine) into aspartic acid          (00:02:35)
[INFO]       Auto_mut: Mutating residue number 166 from chain A (leucine) into glutamic acid       (00:02:35)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (valine) into arginine               (00:03:41)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (valine) into lysine                 (00:03:42)
[INFO]       Auto_mut: Mutating residue number 166 from chain A (leucine) into lysine              (00:03:43)
[INFO]       Auto_mut: Mutating residue number 166 from chain A (leucine) into aspartic acid       (00:04:49)
[INFO]       Auto_mut: Mutating residue number 147 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 147 from chain A (phenylalanine) into glutamic acid (00:04:51)
[INFO]       Auto_mut: Mutating residue number 147 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 147 from chain A (phenylalanine) into aspartic acid (00:04:54)
[INFO]       Auto_mut: Mutating residue number 166 from chain A (leucine) into arginine            (00:05:55)
[INFO]       Auto_mut: Mutating residue number 147 from chain A (phenylalanine) into arginine      (00:06:00)
[INFO]       Auto_mut: Mutating residue number 147 from chain A (phenylalanine) into lysine        (00:06:02)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (glycine) into glutamic acid         (00:07:06)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (glycine) into aspartic acid         (00:07:13)
[INFO]       Auto_mut: Mutating residue number 115 from chain A (valine) into glutamic acid        (00:07:18)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (glycine) into lysine                (00:08:12)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (glycine) into arginine              (00:08:17)
[INFO]       Auto_mut: Mutating residue number 115 from chain A (valine) into lysine               (00:08:27)
[INFO]       Auto_mut: Mutating residue number 115 from chain A (valine) into aspartic acid        (00:09:20)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (methionine) into glutamic acid    (00:09:24)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (methionine) into aspartic acid    (00:09:33)
[INFO]       Auto_mut: Mutating residue number 115 from chain A (valine) into arginine             (00:10:25)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (methionine) into lysine           (00:10:34)
[INFO]       Auto_mut: Mutating residue number 111 from chain A (methionine) into arginine         (00:10:38)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.9191 kcal/mol, Difference in average score from  
                       the base case: -0.0791                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (valine) into lysine:      
                       Energy difference: -0.4218 kcal/mol, Difference in average score from the   
                       base case: -0.0756                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.9463 kcal/mol, Difference in average score from  
                       the base case: -0.0844                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (valine) into arginine:    
                       Energy difference: -1.3973 kcal/mol, Difference in average score from the   
                       base case: -0.0641                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 166 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.3389 kcal/mol, Difference in average score from  
                       the base case: -0.0620                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 166 from chain A (leucine) into lysine:   
                       Energy difference: 0.1385 kcal/mol, Difference in average score from the    
                       base case: -0.0697                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 166 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.0022 kcal/mol, Difference in average score from  
                       the base case: -0.0703                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 166 from chain A (leucine) into arginine: 
                       Energy difference: 0.1077 kcal/mol, Difference in average score from the    
                       base case: -0.0727                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 147 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.4961 kcal/mol, Difference in average    
                       score from the base case: -0.0818                                           (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 147 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.0180 kcal/mol, Difference in average score     
                       from the base case: -0.0729                                                 (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 147 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.8807 kcal/mol, Difference in average    
                       score from the base case: -0.0919                                           (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 147 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.2669 kcal/mol, Difference in average score   
                       from the base case: -0.0859                                                 (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (glycine) into glutamic    
                       acid: Energy difference: 2.0003 kcal/mol, Difference in average score from  
                       the base case: -0.0451                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (glycine) into lysine:     
                       Energy difference: 0.8789 kcal/mol, Difference in average score from the    
                       base case: -0.0427                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (glycine) into aspartic    
                       acid: Energy difference: 1.9792 kcal/mol, Difference in average score from  
                       the base case: -0.0414                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (glycine) into arginine:   
                       Energy difference: 1.3377 kcal/mol, Difference in average score from the    
                       base case: -0.0545                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain A (valine) into glutamic   
                       acid: Energy difference: 2.3920 kcal/mol, Difference in average score from  
                       the base case: -0.0213                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain A (valine) into lysine:    
                       Energy difference: 2.4012 kcal/mol, Difference in average score from the    
                       base case: -0.0253                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain A (valine) into aspartic   
                       acid: Energy difference: 3.1826 kcal/mol, Difference in average score from  
                       the base case: -0.0273                                                      (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 115 from chain A (valine) into arginine:  
                       Energy difference: 1.4607 kcal/mol, Difference in average score from the    
                       base case: -0.0199                                                          (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (methionine) into        
                       glutamic acid: Energy difference: 1.4352 kcal/mol, Difference in average    
                       score from the base case: -0.0282                                           (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (methionine) into        
                       lysine: Energy difference: 0.0130 kcal/mol, Difference in average score     
                       from the base case: -0.0277                                                 (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (methionine) into        
                       aspartic acid: Energy difference: 2.3086 kcal/mol, Difference in average    
                       score from the base case: -0.0274                                           (00:12:03)
[INFO]       Auto_mut: Effect of mutation residue number 111 from chain A (methionine) into        
                       arginine: Energy difference: 0.4586 kcal/mol, Difference in average score   
                       from the base case: -0.0383                                                 (00:12:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:08)
Show buried residues
Minimal score value
-3.7076
Maximal score value
0.7009
Average score
-1.1835
Total score value
-220.1394
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 0.7009
2 G A 0.5314
3 S A 0.0547
4 L A 0.1028
5 N A 0.0000
6 C A 0.0000
7 I A 0.0000
8 V A 0.0000
9 A A -0.0141
10 V A 0.0000
11 S A 0.0000
12 Q A -2.2072
13 N A -1.5674
14 M A -0.8774
15 G A 0.0000
16 I A -0.3148
17 G A -1.4365
18 K A -2.6053
19 N A -2.8010
20 G A -2.2371
21 D A -2.5110
22 L A -1.0273
23 P A 0.0000
24 W A 0.0000
25 P A -0.8598
26 P A -0.9432
27 L A 0.0000
28 R A -2.5298
29 N A -1.9895
30 E A 0.0000
31 F A -1.3034
32 R A -2.7005
33 Y A 0.0000
34 F A -1.0083
35 Q A -2.1317
36 R A -2.4276
37 M A -1.1063
38 T A 0.0000
39 T A -1.3788
40 T A -0.9543
41 S A -1.0294
42 S A -0.5638
43 V A -0.8395
44 E A -2.1917
45 G A -2.1311
46 K A -2.2251
47 Q A -2.0248
48 N A 0.0000
49 L A 0.0000
50 V A 0.0000
51 I A 0.0000
52 M A 0.0000
53 G A -0.7790
54 K A -1.7696
55 K A -1.8568
56 T A -0.9430
57 W A 0.0000
58 F A -0.1302
59 S A -0.9562
60 I A -1.0855
61 P A -1.7399
62 E A -3.1644
63 K A -3.3756
64 N A -3.2608
65 R A -2.5386
66 P A -2.0945
67 L A 0.0000
68 K A -2.3677
69 G A -1.6124
70 R A -1.2464
71 I A -0.7532
72 N A 0.0000
73 L A 0.0000
74 V A 0.0000
75 L A -1.4267
76 S A 0.0000
77 R A -3.5791
78 E A -3.5797
79 L A -2.8729
80 K A -3.3913
81 E A -3.0282
82 P A -1.7779
83 P A 0.0000
84 Q A -2.0193
85 G A -1.7558
86 A A 0.0000
87 H A -1.2909
88 F A -0.2672
89 L A -1.2511
90 S A 0.0000
91 R A -3.0981
92 S A -2.1615
93 L A 0.0000
94 D A -2.4244
95 D A -2.8132
96 A A 0.0000
97 L A -1.5354
98 K A -2.9396
99 L A -2.0403
100 T A 0.0000
101 E A -2.6447
102 Q A -2.4746
103 P A -2.1287
104 E A -2.4795
105 L A 0.0000
106 A A -2.1115
107 N A -2.5821
108 K A -2.6703
109 V A 0.0000
110 D A 0.0000
111 M A 0.1097
112 V A 0.0000
113 W A 0.0000
114 I A 0.0000
115 V A 0.2067
116 G A 0.0000
117 G A -0.5368
118 S A -0.3171
119 S A -0.9370
120 V A 0.0000
121 Y A 0.0000
122 K A -2.6266
123 E A -2.2955
124 A A 0.0000
125 M A 0.0000
126 N A -2.5128
127 H A -1.8349
128 P A -1.6422
129 G A -1.8180
130 H A -1.9420
131 L A 0.0000
132 K A -0.6937
133 L A 0.0000
134 F A 0.0000
135 V A 0.0000
136 T A 0.0000
137 R A -1.4882
138 I A 0.0000
139 M A -1.5908
140 Q A -2.0226
141 D A -2.8065
142 F A -2.1226
143 E A -2.7163
144 S A -2.2668
145 D A -2.5464
146 T A -0.9061
147 F A 0.5499
148 F A 0.0000
149 P A -1.1657
150 E A -1.9559
151 I A -2.0866
152 D A -2.8546
153 L A -1.2044
154 E A -2.7458
155 K A -3.7076
156 Y A 0.0000
157 K A -1.9371
158 L A 0.1096
159 L A -0.4237
160 P A -0.9463
161 E A -1.6254
162 Y A -0.5665
163 P A -0.4916
164 G A -0.3140
165 V A 0.0430
166 L A 0.5668
167 S A -0.7695
168 D A -1.4115
169 V A -1.0253
170 Q A -1.6819
171 E A -3.0380
172 E A -2.9564
173 K A -2.9604
174 G A -2.1930
175 I A 0.0000
176 K A -2.6281
177 Y A 0.0000
178 K A -1.3542
179 F A 0.0000
180 E A 0.0000
181 V A 0.0000
182 Y A 0.0000
183 E A -1.3292
184 K A 0.0000
185 N A -3.0921
186 D A -3.0717
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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
VR1A -1.3973 -0.0641 View CSV PDB
VK1A -0.4218 -0.0756 View CSV PDB
LD166A 0.0022 -0.0703 View CSV PDB
FK147A 0.018 -0.0729 View CSV PDB
MK111A 0.013 -0.0277 View CSV PDB
LR166A 0.1077 -0.0727 View CSV PDB
FR147A 0.2669 -0.0859 View CSV PDB
MR111A 0.4586 -0.0383 View CSV PDB
GK2A 0.8789 -0.0427 View CSV PDB
GR2A 1.3377 -0.0545 View CSV PDB
VR115A 1.4607 -0.0199 View CSV PDB
VK115A 2.4012 -0.0253 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018