Project name: 252d6eb141c8f11

Status: done

Started: 2026-04-03 05:28:45
Settings
Chain sequence(s) A: ATGGYVQQATGQASFTMYSSGCGSSPACGKKAASGFTAAINQLAFGSAPGLGAGDACGRCFALTGNHDPYSSPNYTGPFGQTIVVKVTDLCPPVQQGNQEFCGQTTTTSSNNPPTNQHGMPFHFDICEDTGGSSAKFFPSSGHGALTGTFTTEVSCSQWSGSSDGGQQLWNNGACLSSGETAPNWPSTACGNKKGTAPS
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                                          (00:00:36)
[INFO]       Auto_mut: Residue number 67 from chain A and a score of 0.884 (tyrosine) selected for 
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Residue number 48 from chain A and a score of 0.571 (leucine) selected for  
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Residue number 153 from chain A and a score of 0.066 (leucine) selected for 
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 0.065 (valine) selected for    
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Residue number 80 from chain A and a score of 0.016 (valine) selected for   
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Residue number 49 from chain A and a score of 0.002 (glycine) selected for  
                       automated muatation                                                         (00:00:36)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (tyrosine) into aspartic acid       (00:00:36)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (leucine) into glutamic acid        (00:00:36)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (tyrosine) into glutamic acid       (00:00:36)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (leucine) into lysine               (00:01:02)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (tyrosine) into arginine            (00:01:05)
[INFO]       Auto_mut: Mutating residue number 67 from chain A (tyrosine) into lysine              (00:01:06)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (leucine) into aspartic acid        (00:01:37)
[INFO]       Auto_mut: Mutating residue number 153 from chain A (leucine) into glutamic acid       (00:01:40)
[INFO]       Auto_mut: Mutating residue number 153 from chain A (leucine) into aspartic acid       (00:01:54)
[INFO]       Auto_mut: Mutating residue number 48 from chain A (leucine) into arginine             (00:02:00)
[INFO]       Auto_mut: Mutating residue number 153 from chain A (leucine) into lysine              (00:02:05)
[INFO]       Auto_mut: Mutating residue number 153 from chain A (leucine) into arginine            (00:02:17)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (valine) into glutamic acid          (00:02:25)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (valine) into aspartic acid          (00:02:34)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (valine) into glutamic acid         (00:02:41)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (valine) into lysine                 (00:02:54)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (valine) into arginine               (00:02:56)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (valine) into lysine                (00:03:04)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (valine) into aspartic acid         (00:03:24)
[INFO]       Auto_mut: Mutating residue number 49 from chain A (glycine) into glutamic acid        (00:03:28)
[INFO]       Auto_mut: Mutating residue number 49 from chain A (glycine) into aspartic acid        (00:03:45)
[INFO]       Auto_mut: Mutating residue number 80 from chain A (valine) into arginine              (00:03:45)
[INFO]       Auto_mut: Mutating residue number 49 from chain A (glycine) into lysine               (00:03:53)
[INFO]       Auto_mut: Mutating residue number 49 from chain A (glycine) into arginine             (00:04:07)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.8520 kcal/mol, Difference in average score from  
                       the base case: -0.0658                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.9834 kcal/mol, Difference in average score from the    
                       base case: -0.0582                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.9824 kcal/mol, Difference in average score from  
                       the base case: -0.0684                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 67 from chain A (tyrosine) into arginine: 
                       Energy difference: -2.0152 kcal/mol, Difference in average score from the   
                       base case: -0.0555                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.8062 kcal/mol, Difference in average score from  
                       the base case: -0.0553                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (leucine) into lysine:    
                       Energy difference: 0.6959 kcal/mol, Difference in average score from the    
                       base case: -0.0554                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.8663 kcal/mol, Difference in average score from  
                       the base case: -0.0629                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 48 from chain A (leucine) into arginine:  
                       Energy difference: 0.5960 kcal/mol, Difference in average score from the    
                       base case: -0.0577                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 153 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.1454 kcal/mol, Difference in average score from  
                       the base case: -0.0578                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 153 from chain A (leucine) into lysine:   
                       Energy difference: 0.3811 kcal/mol, Difference in average score from the    
                       base case: -0.0480                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 153 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.4088 kcal/mol, Difference in average score from  
                       the base case: -0.0584                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 153 from chain A (leucine) into arginine: 
                       Energy difference: 0.1727 kcal/mol, Difference in average score from the    
                       base case: -0.0506                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.3294 kcal/mol, Difference in average score from  
                       the base case: -0.0173                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (valine) into lysine:      
                       Energy difference: -0.5426 kcal/mol, Difference in average score from the   
                       base case: -0.0213                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.0521 kcal/mol, Difference in average score from  
                       the base case: -0.0253                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (valine) into arginine:    
                       Energy difference: -0.0326 kcal/mol, Difference in average score from the   
                       base case: -0.0254                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (valine) into glutamic    
                       acid: Energy difference: 1.9070 kcal/mol, Difference in average score from  
                       the base case: -0.0158                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (valine) into lysine:     
                       Energy difference: 0.8054 kcal/mol, Difference in average score from the    
                       base case: -0.0155                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (valine) into aspartic    
                       acid: Energy difference: 2.6609 kcal/mol, Difference in average score from  
                       the base case: -0.0169                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 80 from chain A (valine) into arginine:   
                       Energy difference: 1.4460 kcal/mol, Difference in average score from the    
                       base case: -0.0162                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 49 from chain A (glycine) into glutamic   
                       acid: Energy difference: 2.2800 kcal/mol, Difference in average score from  
                       the base case: -0.0089                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 49 from chain A (glycine) into lysine:    
                       Energy difference: 3.0695 kcal/mol, Difference in average score from the    
                       base case: -0.0255                                                          (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 49 from chain A (glycine) into aspartic   
                       acid: Energy difference: 1.4588 kcal/mol, Difference in average score from  
                       the base case: -0.0124                                                      (00:04:37)
[INFO]       Auto_mut: Effect of mutation residue number 49 from chain A (glycine) into arginine:  
                       Energy difference: 2.6166 kcal/mol, Difference in average score from the    
                       base case: -0.0433                                                          (00:04:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:41)
Show buried residues
Minimal score value
-2.7449
Maximal score value
0.8839
Average score
-0.5401
Total score value
-97.2257
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 A A -0.2754
2 T A -0.3784
3 G A -0.6187
4 G A -0.4675
5 Y A 0.0000
6 V A 0.0649
7 Q A 0.0000
8 Q A -1.3306
9 A A -0.9031
10 T A -0.8052
11 G A -0.8957
12 Q A -1.1367
13 A A 0.0000
14 S A 0.0000
15 F A 0.0000
16 T A -0.0910
17 M A -0.3163
18 Y A -0.6472
19 S A -1.3390
20 G A -1.4202
21 C A 0.0000
22 G A -0.9873
23 S A -0.5559
24 P A 0.0000
25 A A -0.0460
26 C A 0.0000
27 G A 0.0000
28 K A -0.9960
29 A A -1.0430
30 A A 0.0000
31 S A -1.0993
32 G A -0.6421
33 F A -0.2372
34 T A 0.0000
35 A A 0.0000
36 A A 0.0000
37 I A 0.0000
38 N A 0.0000
39 Q A 0.0000
40 L A 0.0000
41 A A 0.0000
42 F A 0.0000
43 G A 0.0000
44 S A 0.0000
45 A A -0.1622
46 P A -0.2335
47 G A -0.0492
48 L A 0.5712
49 G A 0.0018
50 A A 0.0000
51 G A 0.0000
52 D A 0.0000
53 A A 0.0000
54 C A 0.0000
55 G A 0.0000
56 R A 0.0000
57 C A 0.0000
58 F A 0.0000
59 A A -0.0108
60 L A 0.0000
61 T A -0.7942
62 G A 0.0000
63 N A -1.6155
64 H A -1.2367
65 D A 0.0000
66 P A -0.0175
67 Y A 0.8839
68 S A -0.0542
69 P A -0.6101
70 N A -1.2334
71 Y A -0.4863
72 T A -0.6837
73 G A -0.6451
74 P A -0.5877
75 F A -0.7957
76 G A -1.2580
77 Q A -1.5023
78 T A -0.7636
79 I A 0.0000
80 V A 0.0156
81 V A 0.0000
82 K A 0.0000
83 V A 0.0000
84 T A 0.0000
85 D A -0.2639
86 L A -0.0161
87 C A 0.0000
88 P A -0.7350
89 V A -1.0958
90 Q A -1.7952
91 G A -1.6264
92 N A -1.7239
93 Q A -2.2668
94 E A -1.8229
95 F A -1.0085
96 C A 0.0000
97 G A -1.4612
98 Q A 0.0000
99 T A -0.6700
100 T A -0.6753
101 S A -0.9671
102 N A -1.5328
103 P A -0.8642
104 T A -0.9696
105 N A 0.0000
106 Q A -1.8176
107 H A -0.9099
108 G A -0.9888
109 M A -0.6475
110 P A -0.5965
111 F A 0.0000
112 H A 0.0000
113 F A 0.0000
114 D A -0.2133
115 I A 0.0000
116 C A 0.0000
117 E A -2.5777
118 D A -2.7449
119 T A -1.5172
120 G A -1.2864
121 G A 0.0000
122 S A 0.0000
123 A A -1.2005
124 K A -1.4373
125 F A 0.0000
126 F A 0.0000
127 P A -0.7139
128 S A -0.5544
129 G A -0.7383
130 H A -0.4397
131 G A -0.2958
132 A A -0.0253
133 L A 0.0000
134 T A -0.8433
135 G A -0.9889
136 T A -0.7751
137 F A 0.0000
138 T A -0.3893
139 E A 0.0000
140 V A -0.2773
141 S A -0.7546
142 C A -0.7294
143 S A -0.9319
144 Q A -1.2533
145 W A 0.0000
146 S A -0.6545
147 G A -1.1264
148 S A -1.3792
149 D A -2.3900
150 G A -1.6362
151 G A -1.2680
152 Q A -1.4240
153 L A 0.0658
154 W A -0.0807
155 N A -1.2298
156 G A -0.8662
157 A A 0.0000
158 C A -0.4521
159 L A 0.0000
160 S A -0.4389
161 G A 0.0000
162 E A -1.2260
163 T A -0.7646
164 A A -0.8164
165 P A -1.0412
166 N A -1.7116
167 W A 0.0000
168 P A -0.9268
169 S A -0.5963
170 T A -0.3977
171 A A -0.2329
172 C A -0.2208
173 G A -0.3274
174 N A -0.5141
175 K A -0.5526
176 G A -0.6862
177 T A -0.6652
178 A A 0.0000
179 P A -0.4714
180 S A -0.6174
Download PDB file
View in 3Dmol
Play the video

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
YR67A -2.0152 -0.0555 View CSV PDB
VK6A -0.5426 -0.0213 View CSV PDB
VR6A -0.0326 -0.0254 View CSV PDB
LR153A 0.1727 -0.0506 View CSV PDB
LK153A 0.3811 -0.048 View CSV PDB
LR48A 0.596 -0.0577 View CSV PDB
LK48A 0.6959 -0.0554 View CSV PDB
YK67A 0.9834 -0.0582 View CSV PDB
VK80A 0.8054 -0.0155 View CSV PDB
GR49A 2.6166 -0.0433 View CSV PDB
VR80A 1.446 -0.0162 View CSV PDB
GD49A 1.4588 -0.0124 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018