Project name: WB17_model 0

Status: done

Started: 2026-05-08 02:15:10
Settings
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCRASQGPTSYLAWYQQKPGKAPKLLIYATKTLQSGVPSRFSGSGSGTDFTLTISRLQPEDFATYYCQQLNSYPLTFGGGTKVEIKGGGGSGGGGSGGGGSGGGGSQVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARGVLDVWGQGTTVTVSS
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                                          (00:06:04)
[INFO]       Auto_mut: Residue number 227 from chain A and a score of 1.639 (valine) selected for  
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Residue number 138 from chain A and a score of 1.336 (valine) selected for  
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Residue number 32 from chain A and a score of 1.138 (tyrosine) selected for 
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Residue number 91 from chain A and a score of 0.904 (leucine) selected for  
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Residue number 94 from chain A and a score of 0.862 (tyrosine) selected for 
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Residue number 132 from chain A and a score of 0.679 (valine) selected for  
                       automated muatation                                                         (00:06:08)
[INFO]       Auto_mut: Mutating residue number 227 from chain A (valine) into glutamic acid        (00:06:08)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (valine) into glutamic acid        (00:06:08)
[INFO]       Auto_mut: Mutating residue number 227 from chain A (valine) into aspartic acid        (00:06:08)
[INFO]       Auto_mut: Mutating residue number 227 from chain A (valine) into arginine             (00:09:34)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (valine) into lysine               (00:09:37)
[INFO]       Auto_mut: Mutating residue number 227 from chain A (valine) into lysine               (00:09:54)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (valine) into aspartic acid        (00:12:39)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into glutamic acid       (00:12:52)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into aspartic acid       (00:13:43)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (valine) into arginine             (00:14:56)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into lysine              (00:15:13)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into arginine            (00:15:29)
[INFO]       Auto_mut: Mutating residue number 91 from chain A (leucine) into glutamic acid        (00:16:18)
[INFO]       Auto_mut: Mutating residue number 91 from chain A (leucine) into aspartic acid        (00:16:32)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into glutamic acid       (00:16:44)
[INFO]       Auto_mut: Mutating residue number 91 from chain A (leucine) into lysine               (00:17:23)
[INFO]       Auto_mut: Mutating residue number 91 from chain A (leucine) into arginine             (00:17:33)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into lysine              (00:17:51)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into aspartic acid       (00:18:46)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into glutamic acid        (00:18:54)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into aspartic acid        (00:19:02)
[INFO]       Auto_mut: Mutating residue number 94 from chain A (tyrosine) into arginine            (00:19:52)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into arginine             (00:20:05)
[INFO]       Auto_mut: Mutating residue number 132 from chain A (valine) into lysine               (00:20:13)
[INFO]       Auto_mut: Effect of mutation residue number 227 from chain A (valine) into glutamic   
                       acid: Energy difference: -1.1524 kcal/mol, Difference in average score from 
                       the base case: -0.0334                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 227 from chain A (valine) into lysine:    
                       Energy difference: -1.5772 kcal/mol, Difference in average score from the   
                       base case: -0.0247                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 227 from chain A (valine) into aspartic   
                       acid: Energy difference: -1.5289 kcal/mol, Difference in average score from 
                       the base case: -0.0314                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 227 from chain A (valine) into arginine:  
                       Energy difference: -2.8555 kcal/mol, Difference in average score from the   
                       base case: -0.0318                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0980 kcal/mol, Difference in average score from  
                       the base case: -0.0342                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (valine) into lysine:    
                       Energy difference: -0.3256 kcal/mol, Difference in average score from the   
                       base case: -0.0326                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.2964 kcal/mol, Difference in average score from  
                       the base case: -0.0347                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (valine) into arginine:  
                       Energy difference: -0.4830 kcal/mol, Difference in average score from the   
                       base case: -0.0342                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.1509 kcal/mol, Difference in average score from  
                       the base case: -0.0152                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.4823 kcal/mol, Difference in average score from the   
                       base case: -0.0392                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.3343 kcal/mol, Difference in average score from  
                       the base case: -0.0343                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.7528 kcal/mol, Difference in average score from the   
                       base case: -0.0351                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 91 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.6599 kcal/mol, Difference in average score from  
                       the base case: -0.0281                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 91 from chain A (leucine) into lysine:    
                       Energy difference: 2.2093 kcal/mol, Difference in average score from the    
                       base case: 0.0008                                                           (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 91 from chain A (leucine) into aspartic   
                       acid: Energy difference: 2.5421 kcal/mol, Difference in average score from  
                       the base case: -0.0270                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 91 from chain A (leucine) into arginine:  
                       Energy difference: 2.1581 kcal/mol, Difference in average score from the    
                       base case: 0.0007                                                           (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.9547 kcal/mol, Difference in average score from  
                       the base case: -0.0191                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into lysine:   
                       Energy difference: 1.3627 kcal/mol, Difference in average score from the    
                       base case: -0.0208                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.7413 kcal/mol, Difference in average score from  
                       the base case: -0.0140                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 94 from chain A (tyrosine) into arginine: 
                       Energy difference: 1.0842 kcal/mol, Difference in average score from the    
                       base case: -0.0270                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into glutamic   
                       acid: Energy difference: 0.0468 kcal/mol, Difference in average score from  
                       the base case: -0.0219                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into lysine:    
                       Energy difference: -0.4977 kcal/mol, Difference in average score from the   
                       base case: -0.0247                                                          (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.3790 kcal/mol, Difference in average score from  
                       the base case: -0.0240                                                      (00:21:34)
[INFO]       Auto_mut: Effect of mutation residue number 132 from chain A (valine) into arginine:  
                       Energy difference: -0.4941 kcal/mol, Difference in average score from the   
                       base case: -0.0252                                                          (00:21:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:38)
Show buried residues
Minimal score value
-2.8124
Maximal score value
1.6388
Average score
-0.7088
Total score value
-170.8137
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 D A -2.0077
2 I A -1.7731
3 Q A -2.1873
4 M A 0.0000
5 T A -1.2884
6 Q A -0.9758
7 S A -0.8068
8 P A -0.6021
9 S A -0.8485
10 S A -1.1094
11 L A -0.7742
12 S A -1.1969
13 A A 0.0000
14 S A -0.5942
15 V A 0.3246
16 G A -1.0681
17 D A -2.0791
18 R A -2.8124
19 V A 0.0000
20 T A -0.6192
21 I A 0.0000
22 T A -0.8021
23 C A 0.0000
24 R A -2.6278
25 A A 0.0000
26 S A -1.9986
27 Q A -2.3234
28 G A -1.7108
29 P A -1.0445
30 T A 0.0000
31 S A 0.0781
32 Y A 1.1379
33 L A 0.0000
34 A A 0.0000
35 W A 0.0000
36 Y A 0.0000
37 Q A 0.0000
38 Q A 0.0000
39 K A -1.6593
40 P A -1.3011
41 G A -1.6748
42 K A -2.5621
43 A A -1.5933
44 P A 0.0000
45 K A -1.4072
46 L A 0.0000
47 L A 0.0000
48 I A 0.0000
49 Y A 0.6386
50 A A 0.4366
51 T A 0.0000
52 K A -1.4935
53 T A -0.5518
54 L A -0.1018
55 Q A -0.4642
56 S A -0.3915
57 G A -0.5234
58 V A -0.3512
59 P A -0.3292
60 S A -0.5724
61 R A -1.1548
62 F A 0.0000
63 S A -0.6811
64 G A -0.8631
65 S A -1.1555
66 G A -1.3488
67 S A -0.9378
68 G A -1.3089
69 T A -1.7938
70 D A -2.0534
71 F A 0.0000
72 T A -0.9239
73 L A 0.0000
74 T A -0.8200
75 I A 0.0000
76 S A -2.0841
77 R A -2.7662
78 L A 0.0000
79 Q A -1.1403
80 P A -0.5713
81 E A -1.2921
82 D A 0.0000
83 F A -0.5951
84 A A 0.0000
85 T A -1.0180
86 Y A 0.0000
87 Y A 0.0000
88 C A 0.0000
89 Q A 0.0000
90 Q A 0.0000
91 L A 0.9036
92 N A -0.0301
93 S A 0.0782
94 Y A 0.8624
95 P A -0.0951
96 L A 0.0000
97 T A -0.5774
98 F A 0.0000
99 G A 0.0000
100 G A -1.2578
101 G A 0.0000
102 T A 0.0000
103 K A -1.9666
104 V A 0.0000
105 E A -1.7323
106 I A -0.1786
107 K A -1.6589
108 G A -1.5589
109 G A -1.4369
110 G A -1.2910
111 G A -1.2823
112 S A -1.0284
113 G A -1.1035
114 G A -1.1837
115 G A -1.2006
116 G A -1.1279
117 S A -0.9265
118 G A -1.0189
119 G A -1.1787
120 G A -1.1200
121 G A -1.0100
122 S A -0.9689
123 G A -1.0551
124 G A -1.2942
125 G A -1.2873
126 G A -1.2509
127 S A -1.1839
128 Q A -1.4761
129 V A -0.2971
130 Q A -0.6779
131 L A 0.0000
132 V A 0.6788
133 E A 0.0000
134 S A -0.4693
135 G A -0.9639
136 G A -0.3632
137 G A 0.3238
138 V A 1.3362
139 V A 0.0000
140 Q A -1.8393
141 P A -2.1146
142 G A -2.0944
143 R A -2.7623
144 S A -2.0533
145 L A -1.2955
146 R A -1.9648
147 L A 0.0000
148 S A -0.4243
149 C A 0.0000
150 A A -0.2146
151 A A 0.0000
152 S A -0.6510
153 G A -0.6239
154 F A -0.2522
155 T A -0.3930
156 F A 0.0000
157 S A -0.9483
158 N A -1.0718
159 Y A 0.1851
160 G A -0.0096
161 M A 0.0000
162 H A 0.0000
163 W A 0.0000
164 V A 0.0000
165 R A 0.0000
166 Q A -0.7719
167 A A -1.2024
168 P A -1.1668
169 G A -1.4531
170 K A -2.2594
171 G A -1.4140
172 L A 0.0000
173 E A -0.9232
174 W A 0.0000
175 V A 0.0000
176 A A 0.0000
177 V A 0.0000
178 I A 0.0000
179 S A -0.7578
180 Y A -0.2580
181 D A -1.8465
182 G A -1.4273
183 S A -1.3832
184 N A -1.7583
185 K A -1.2110
186 Y A -0.1773
187 Y A -0.5994
188 A A 0.0000
189 D A -2.4163
190 S A -1.7292
191 V A 0.0000
192 K A -2.5329
193 G A -1.7703
194 R A -1.5287
195 F A 0.0000
196 T A -0.8641
197 I A 0.0000
198 S A -0.5065
199 R A -1.0533
200 D A -1.7717
201 N A -1.9455
202 S A -1.6171
203 K A -2.4000
204 N A -1.7679
205 T A -1.0612
206 L A 0.0000
207 Y A -0.5274
208 L A 0.0000
209 Q A -1.1304
210 M A 0.0000
211 N A -1.8918
212 S A -1.7655
213 L A 0.0000
214 R A -2.7485
215 A A -1.8121
216 E A -2.3312
217 D A 0.0000
218 T A -0.6560
219 A A 0.0000
220 V A 0.1376
221 Y A 0.0000
222 Y A 0.0000
223 C A 0.0000
224 A A 0.0000
225 R A 0.1652
226 G A 0.6386
227 V A 1.6388
228 L A 0.0000
229 D A -0.0832
230 V A 0.0449
231 W A -0.4661
232 G A 0.0000
233 Q A -1.4036
234 G A 0.0000
235 T A -0.1749
236 T A 0.1949
237 V A 0.0000
238 T A 0.0130
239 V A 0.0000
240 S A -0.6857
241 S A -0.6797
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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
VR227A -2.8555 -0.0318 View CSV PDB
VD227A -1.5289 -0.0314 View CSV PDB
YR32A -0.7528 -0.0351 View CSV PDB
YK32A -0.4823 -0.0392 View CSV PDB
VR138A -0.483 -0.0342 View CSV PDB
VK138A -0.3256 -0.0326 View CSV PDB
VR132A -0.4941 -0.0252 View CSV PDB
VK132A -0.4977 -0.0247 View CSV PDB
LE91A 0.6599 -0.0281 View CSV PDB
YR94A 1.0842 -0.027 View CSV PDB
YK94A 1.3627 -0.0208 View CSV PDB
LD91A 2.5421 -0.027 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018