Project name: APNB

Status: done

Started: 2025-10-27 03:28:21
Settings
Chain sequence(s) A: DVQLQESGGDSVQAGGSLRLSCAASAATYCMYDMKWYRQAPGKGREFVSAIDKNGSTRYSDSVKGRFTISQDYAKNTVYLQMNSLKPEDTAMYYCNCGSYGSTWPWGQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYLEHHHHHH
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                                          (00:07:12)
[INFO]       Auto_mut: Residue number 29 from chain A and a score of 1.062 (tyrosine) selected for 
                       automated muatation                                                         (00:07:13)
[INFO]       Auto_mut: Residue number 123 from chain A and a score of 0.967 (leucine) selected for 
                       automated muatation                                                         (00:07:13)
[INFO]       Auto_mut: Residue number 100 from chain A and a score of 0.896 (tyrosine) selected    
                       for automated muatation                                                     (00:07:13)
[INFO]       Auto_mut: Residue number 28 from chain A and a score of 0.532 (threonine) selected    
                       for automated muatation                                                     (00:07:13)
[INFO]       Auto_mut: Residue number 126 from chain A and a score of 0.303 (leucine) selected for 
                       automated muatation                                                         (00:07:13)
[INFO]       Auto_mut: Residue number 32 from chain A and a score of 0.217 (tyrosine) selected for 
                       automated muatation                                                         (00:07:13)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (tyrosine) into glutamic acid       (00:07:13)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (tyrosine) into aspartic acid       (00:07:13)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into glutamic acid       (00:07:13)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (tyrosine) into arginine            (00:10:45)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into lysine              (00:10:48)
[INFO]       Auto_mut: Mutating residue number 29 from chain A (tyrosine) into lysine              (00:10:51)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into aspartic acid       (00:14:50)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (tyrosine) into glutamic acid      (00:14:51)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (tyrosine) into aspartic acid      (00:15:03)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into arginine            (00:18:09)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (tyrosine) into arginine           (00:18:31)
[INFO]       Auto_mut: Mutating residue number 100 from chain A (tyrosine) into lysine             (00:18:40)
[INFO]       Auto_mut: Mutating residue number 28 from chain A (threonine) into glutamic acid      (00:22:01)
[INFO]       Auto_mut: Mutating residue number 28 from chain A (threonine) into aspartic acid      (00:22:10)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (leucine) into glutamic acid       (00:22:30)
[INFO]       Auto_mut: Mutating residue number 28 from chain A (threonine) into lysine             (00:25:29)
[INFO]       Auto_mut: Mutating residue number 28 from chain A (threonine) into arginine           (00:25:34)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (leucine) into lysine              (00:25:55)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (leucine) into aspartic acid       (00:29:04)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into glutamic acid       (00:29:06)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into aspartic acid       (00:30:24)
[INFO]       Auto_mut: Mutating residue number 126 from chain A (leucine) into arginine            (00:32:24)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into lysine              (00:32:31)
[INFO]       Auto_mut: Mutating residue number 32 from chain A (tyrosine) into arginine            (00:34:22)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: -0.2341 kcal/mol, Difference in average score from 
                       the base case: -0.0366                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.1651 kcal/mol, Difference in average score from the   
                       base case: -0.0338                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 0.3575 kcal/mol, Difference in average score from  
                       the base case: -0.0402                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 29 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.8968 kcal/mol, Difference in average score from the   
                       base case: -0.0501                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6368 kcal/mol, Difference in average score from  
                       the base case: -0.0590                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into lysine:   
                       Energy difference: 0.2851 kcal/mol, Difference in average score from the    
                       base case: -0.0240                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.0929 kcal/mol, Difference in average score from  
                       the base case: -0.0507                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into arginine: 
                       Energy difference: 0.3505 kcal/mol, Difference in average score from the    
                       base case: -0.0267                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: -0.1633 kcal/mol, Difference in average score from 
                       the base case: -0.0527                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.0590 kcal/mol, Difference in average score from the    
                       base case: -0.0397                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -0.1513 kcal/mol, Difference in average score from 
                       the base case: -0.0515                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 100 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.1464 kcal/mol, Difference in average score   
                       from the base case: -0.0522                                                 (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 28 from chain A (threonine) into glutamic 
                       acid: Energy difference: 0.1519 kcal/mol, Difference in average score from  
                       the base case: -0.0328                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 28 from chain A (threonine) into lysine:  
                       Energy difference: 0.2375 kcal/mol, Difference in average score from the    
                       base case: -0.0281                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 28 from chain A (threonine) into aspartic 
                       acid: Energy difference: -0.9238 kcal/mol, Difference in average score from 
                       the base case: -0.0349                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 28 from chain A (threonine) into          
                       arginine: Energy difference: 0.2768 kcal/mol, Difference in average score   
                       from the base case: -0.0295                                                 (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.3671 kcal/mol, Difference in average score from  
                       the base case: -0.0340                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (leucine) into lysine:   
                       Energy difference: 0.5302 kcal/mol, Difference in average score from the    
                       base case: -0.0086                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.0574 kcal/mol, Difference in average score from  
                       the base case: -0.0334                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 126 from chain A (leucine) into arginine: 
                       Energy difference: 0.5644 kcal/mol, Difference in average score from the    
                       base case: -0.0399                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.3214 kcal/mol, Difference in average score from  
                       the base case: -0.0375                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.0519 kcal/mol, Difference in average score from the   
                       base case: -0.0135                                                          (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.0758 kcal/mol, Difference in average score from  
                       the base case: -0.0066                                                      (00:38:22)
[INFO]       Auto_mut: Effect of mutation residue number 32 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.1729 kcal/mol, Difference in average score from the   
                       base case: -0.0548                                                          (00:38:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:38:29)
Show buried residues
Minimal score value
-4.142
Maximal score value
1.0622
Average score
-1.1104
Total score value
-266.4976
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 -1.7907
2 V A -0.8987
3 Q A -1.3172
4 L A 0.0000
5 Q A -1.4154
6 E A 0.0000
7 S A -1.0636
8 G A -1.0924
9 G A -0.9777
10 D A -1.2868
11 S A -1.1542
12 V A -1.2364
13 Q A -2.0447
14 A A -1.9688
15 G A -1.5198
16 G A -1.1014
17 S A -1.5911
18 L A -1.5268
19 R A -2.4726
20 L A 0.0000
21 S A -0.8566
22 C A 0.0000
23 A A -0.9260
24 A A 0.0000
25 S A -0.6362
26 A A -0.3293
27 A A 0.0000
28 T A 0.5316
29 Y A 1.0622
30 C A 0.0000
31 M A 0.0000
32 Y A 0.2172
33 D A -0.8087
34 M A 0.0000
35 K A -0.4359
36 W A 0.0000
37 Y A -0.2896
38 R A 0.0000
39 Q A -1.3675
40 A A -1.5101
41 P A -1.2987
42 G A -1.8418
43 K A -2.6814
44 G A -2.1157
45 R A -1.9344
46 E A -1.6313
47 F A -0.4906
48 V A 0.0000
49 S A 0.0000
50 A A -0.9887
51 I A 0.0000
52 D A -2.0240
53 K A -1.8963
54 N A -2.2325
55 G A -1.8085
56 S A -1.7202
57 T A -1.6418
58 R A -2.3415
59 Y A -1.7577
60 S A -1.7777
61 D A -2.7033
62 S A -1.7934
63 V A 0.0000
64 K A -2.9048
65 G A -1.8846
66 R A -1.6953
67 F A 0.0000
68 T A -1.3154
69 I A 0.0000
70 S A -0.5162
71 Q A -0.6243
72 D A -0.6751
73 Y A -0.0400
74 A A -0.5883
75 K A -1.7330
76 N A -0.8699
77 T A 0.0000
78 V A 0.0000
79 Y A -0.6920
80 L A 0.0000
81 Q A -1.8082
82 M A 0.0000
83 N A -2.1505
84 S A -1.4047
85 L A 0.0000
86 K A -2.0670
87 P A -2.0254
88 E A -2.1763
89 D A 0.0000
90 T A 0.0000
91 A A 0.0000
92 M A -0.0858
93 Y A 0.0000
94 Y A 0.0000
95 C A 0.0000
96 N A 0.0000
97 C A 0.0000
98 G A 0.1588
99 S A 0.1327
100 Y A 0.8959
101 G A 0.0235
102 S A -0.0979
103 T A 0.1237
104 W A 0.1653
105 P A -0.3011
106 W A -0.1134
107 G A -0.8394
108 Q A -1.3717
109 G A -0.7500
110 T A 0.0000
111 L A -0.4144
112 V A 0.0000
113 A A 0.0000
114 V A 0.0000
115 V A 0.0000
116 K A -2.6347
117 T A -1.9080
118 V A 0.0000
119 E A -1.8402
120 D A -1.6268
121 A A 0.0000
122 F A 0.0000
123 L A 0.9673
124 A A 0.0748
125 L A 0.0000
126 L A 0.3033
127 A A -0.2590
128 L A 0.0000
129 E A -1.3622
130 Q A -1.8099
131 H A -1.8765
132 L A -1.0000
133 G A -1.2947
134 V A 0.0000
135 Q A -1.6125
136 P A -1.1584
137 A A -0.7487
138 D A -1.2604
139 L A 0.0000
140 A A -1.1703
141 A A -1.3191
142 L A 0.0000
143 A A 0.0000
144 E A -2.7888
145 K A -2.8921
146 L A 0.0000
147 N A -2.2666
148 L A -1.5139
149 S A -1.0063
150 Q A -1.2961
151 L A 0.0000
152 L A 0.0000
153 E A -1.2084
154 L A 0.0000
155 G A -1.0999
156 E A -1.1091
157 L A -0.6250
158 L A 0.0000
159 K A -2.0637
160 A A -0.8765
161 A A -0.6509
162 G A -1.0881
163 H A 0.0000
164 P A -0.8357
165 L A 0.0000
166 A A -1.3359
167 P A -1.2336
168 Q A -1.2828
169 V A 0.0000
170 E A -1.6582
171 A A -1.2754
172 L A -1.6545
173 L A 0.0000
174 K A -2.0006
175 E A -2.8191
176 K A -2.4494
177 L A 0.0000
178 K A -2.9692
179 A A -1.8165
180 A A -1.7056
181 S A -1.8322
182 A A 0.0000
183 A A -1.3147
184 E A -2.1926
185 A A 0.0000
186 A A 0.0000
187 G A -0.7643
188 V A 0.0000
189 I A 0.0000
190 F A -0.6972
191 Q A -0.6730
192 A A 0.0000
193 L A 0.0000
194 V A -0.8149
195 K A -2.4279
196 D A -3.1243
197 E A -3.5496
198 E A -3.6758
199 L A -2.7800
200 G A 0.0000
201 K A -3.5207
202 K A -2.9530
203 I A 0.0000
204 L A 0.0000
205 E A -3.4673
206 W A -2.8883
207 A A 0.0000
208 K A -3.6516
209 E A -3.3164
210 F A -2.7317
211 G A -2.6143
212 T A -2.9664
213 E A -3.6693
214 E A -4.0536
215 A A 0.0000
216 K A -4.1420
217 K A -3.8019
218 A A 0.0000
219 I A 0.0000
220 E A -3.3319
221 I A -1.6211
222 A A 0.0000
223 E A -3.0962
224 K A -2.8420
225 A A -1.3700
226 Y A -1.3227
227 E A -2.4586
228 L A -0.4913
229 Y A -0.1744
230 K A -1.4051
231 K A -1.7963
232 Y A -0.2673
233 L A -1.1149
234 E A -3.0534
235 H A -3.0287
236 H A -2.7641
237 H A -3.0977
238 H A -3.1775
239 H A -2.9519
240 H A -2.3201
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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
YR29A -0.8968 -0.0501 View CSV PDB
TD28A -0.9238 -0.0349 View CSV PDB
YR32A -0.1729 -0.0548 View CSV PDB
YE100A -0.1633 -0.0527 View CSV PDB
YD100A -0.1513 -0.0515 View CSV PDB
YE29A -0.2341 -0.0366 View CSV PDB
YK32A -0.0519 -0.0135 View CSV PDB
TE28A 0.1519 -0.0328 View CSV PDB
LE123A 0.6368 -0.059 View CSV PDB
LK123A 0.2851 -0.024 View CSV PDB
LR126A 0.5644 -0.0399 View CSV PDB
LE126A 1.3671 -0.034 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018