Project name: ce353f89e214346

Status: done

Started: 2026-05-16 21:21:12
Settings
Chain sequence(s) A: MNPYEKLLNRKRKWTPVQTTKGKLKYGAEETIYRALAVRNMECPVGAFVSDSLSEIPEKSRELLESNIKDEDNHDLALGYIANAIGVDDKAEAEALRLRDAWIEHPDHTILKALVIERAIFFVLLPFFRFNGDAGLRTVSADISRDEQIHVATNSLVCAELGLKPSQSLDKLRKATINWIMQPLNQIHDDQYLSKKFWLDASDRLMYEGKAPEFNETKAARMPAFFEHANTNLPQYS
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]                                                (00:00:08)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:08)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:08)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:08)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:09)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:33)
[INFO]       Auto_mut: Residue number 225 from chain A and a score of 2.226 (phenylalanine)        
                       selected for automated muatation                                            (00:04:35)
[INFO]       Auto_mut: Residue number 226 from chain A and a score of 1.819 (phenylalanine)        
                       selected for automated muatation                                            (00:04:35)
[INFO]       Auto_mut: Residue number 224 from chain A and a score of 1.177 (alanine) selected for 
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 222 from chain A and a score of 1.091 (methionine) selected  
                       for automated muatation                                                     (00:04:35)
[INFO]       Auto_mut: Residue number 223 from chain A and a score of 0.798 (proline) selected for 
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 44 from chain A and a score of 0.331 (proline) selected for  
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 225 from chain A (phenylalanine) into glutamic acid (00:04:35)
[INFO]       Auto_mut: Mutating residue number 226 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 226 from chain A (phenylalanine) into glutamic acid (00:04:35)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 225 from chain A (phenylalanine) into aspartic acid (00:04:35)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (phenylalanine) into arginine      (00:06:39)
[INFO]       Auto_mut: Mutating residue number 226 from chain A (phenylalanine) into lysine        (00:06:43)
[INFO]       Auto_mut: Mutating residue number 225 from chain A (phenylalanine) into lysine        (00:06:44)
[INFO]       Auto_mut: Mutating residue number 226 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 226 from chain A (phenylalanine) into aspartic acid (00:08:51)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (alanine) into glutamic acid       (00:08:52)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (alanine) into aspartic acid       (00:08:57)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (alanine) into lysine              (00:10:59)
[INFO]       Auto_mut: Mutating residue number 226 from chain A (phenylalanine) into arginine      (00:11:00)
[INFO]       Auto_mut: Mutating residue number 224 from chain A (alanine) into arginine            (00:11:06)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (methionine) into glutamic acid    (00:13:05)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (methionine) into aspartic acid    (00:13:15)
[INFO]       Auto_mut: Mutating residue number 223 from chain A (proline) into glutamic acid       (00:13:17)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (methionine) into arginine         (00:15:16)
[INFO]       Auto_mut: Mutating residue number 222 from chain A (methionine) into lysine           (00:15:27)
[INFO]       Auto_mut: Mutating residue number 223 from chain A (proline) into lysine              (00:15:29)
[INFO]       Auto_mut: Mutating residue number 223 from chain A (proline) into aspartic acid       (00:17:31)
[INFO]       Auto_mut: Mutating residue number 44 from chain A (proline) into glutamic acid        (00:17:36)
[INFO]       Auto_mut: Mutating residue number 44 from chain A (proline) into aspartic acid        (00:17:48)
[INFO]       Auto_mut: Mutating residue number 44 from chain A (proline) into lysine               (00:19:30)
[INFO]       Auto_mut: Mutating residue number 223 from chain A (proline) into arginine            (00:19:37)
[INFO]       Auto_mut: Mutating residue number 44 from chain A (proline) into arginine             (00:19:47)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.4402 kcal/mol, Difference in average    
                       score from the base case: -0.0453                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.2214 kcal/mol, Difference in average score     
                       from the base case: -0.0462                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.7055 kcal/mol, Difference in average    
                       score from the base case: -0.0449                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 225 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.1060 kcal/mol, Difference in average score   
                       from the base case: -0.0468                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.7446 kcal/mol, Difference in average    
                       score from the base case: -0.0379                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.5398 kcal/mol, Difference in average score     
                       from the base case: -0.0382                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.8689 kcal/mol, Difference in average    
                       score from the base case: -0.0370                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.4951 kcal/mol, Difference in average score   
                       from the base case: -0.0402                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (alanine) into glutamic  
                       acid: Energy difference: -0.3601 kcal/mol, Difference in average score from 
                       the base case: -0.0111                                                      (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (alanine) into lysine:   
                       Energy difference: -0.7691 kcal/mol, Difference in average score from the   
                       base case: -0.0091                                                          (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (alanine) into aspartic  
                       acid: Energy difference: -0.6203 kcal/mol, Difference in average score from 
                       the base case: -0.0119                                                      (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 224 from chain A (alanine) into arginine: 
                       Energy difference: -0.6631 kcal/mol, Difference in average score from the   
                       base case: -0.0171                                                          (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.2521 kcal/mol, Difference in average    
                       score from the base case: -0.0253                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (methionine) into        
                       lysine: Energy difference: 0.2659 kcal/mol, Difference in average score     
                       from the base case: -0.0234                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.2104 kcal/mol, Difference in average    
                       score from the base case: -0.0250                                           (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 222 from chain A (methionine) into        
                       arginine: Energy difference: 0.1055 kcal/mol, Difference in average score   
                       from the base case: -0.0252                                                 (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 223 from chain A (proline) into glutamic  
                       acid: Energy difference: 1.0043 kcal/mol, Difference in average score from  
                       the base case: 0.0013                                                       (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 223 from chain A (proline) into lysine:   
                       Energy difference: 1.5106 kcal/mol, Difference in average score from the    
                       base case: -0.0029                                                          (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 223 from chain A (proline) into aspartic  
                       acid: Energy difference: 1.4613 kcal/mol, Difference in average score from  
                       the base case: 0.0045                                                       (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 223 from chain A (proline) into arginine: 
                       Energy difference: 1.9024 kcal/mol, Difference in average score from the    
                       base case: -0.0030                                                          (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 44 from chain A (proline) into glutamic   
                       acid: Energy difference: 2.7473 kcal/mol, Difference in average score from  
                       the base case: -0.0035                                                      (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 44 from chain A (proline) into lysine:    
                       Energy difference: 2.1626 kcal/mol, Difference in average score from the    
                       base case: -0.0111                                                          (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 44 from chain A (proline) into aspartic   
                       acid: Energy difference: 4.9697 kcal/mol, Difference in average score from  
                       the base case: 0.0038                                                       (00:21:44)
[INFO]       Auto_mut: Effect of mutation residue number 44 from chain A (proline) into arginine:  
                       Energy difference: 1.9567 kcal/mol, Difference in average score from the    
                       base case: -0.0109                                                          (00:21:44)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:52)
Show buried residues
Minimal score value
-3.408
Maximal score value
2.2257
Average score
-0.82
Total score value
-194.3341
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 0.3245
2 N A -0.7352
3 P A -0.7253
4 Y A 0.0000
5 E A -2.1873
6 K A -2.0193
7 L A -1.7453
8 L A -2.0314
9 N A -2.8647
10 R A -3.4080
11 K A -3.0408
12 R A -3.2828
13 K A -2.6081
14 W A -1.3607
15 T A -0.5388
16 P A -0.3133
17 V A -0.0974
18 Q A -0.3803
19 T A 0.0000
20 T A -1.1479
21 K A -2.3442
22 G A -1.8589
23 K A -2.0489
24 L A -1.0195
25 K A -0.4259
26 Y A 0.3085
27 G A -0.6359
28 A A 0.0000
29 E A -1.6882
30 E A -2.1427
31 T A 0.0000
32 I A 0.0000
33 Y A -0.9123
34 R A -1.3608
35 A A 0.0000
36 L A 0.0000
37 A A 0.0000
38 V A 0.0000
39 R A -0.4753
40 N A -0.5192
41 M A 0.0000
42 E A 0.0000
43 C A -0.1871
44 P A 0.3308
45 V A 0.0000
46 G A 0.0000
47 A A -0.0753
48 F A 0.0000
49 V A 0.0000
50 S A -1.1650
51 D A -2.0999
52 S A 0.0000
53 L A -1.8780
54 S A -1.7266
55 E A -2.3899
56 I A 0.0000
57 P A -2.1004
58 E A -3.3930
59 K A -3.2809
60 S A 0.0000
61 R A -3.3645
62 E A -3.3206
63 L A 0.0000
64 L A 0.0000
65 E A -2.2871
66 S A -1.6638
67 N A 0.0000
68 I A -1.1774
69 K A -2.4570
70 D A -1.9669
71 E A 0.0000
72 D A -2.4394
73 N A -1.5617
74 H A 0.0000
75 D A -1.2514
76 L A -0.3358
77 A A 0.0000
78 L A 0.0000
79 G A -0.3648
80 Y A -0.2619
81 I A 0.0000
82 A A -0.4218
83 N A -1.2920
84 A A -1.1589
85 I A 0.0000
86 G A -0.3715
87 V A -0.0736
88 D A -1.8196
89 D A -2.8500
90 K A -2.9168
91 A A 0.0000
92 E A -1.8293
93 A A -2.0702
94 E A -2.4205
95 A A 0.0000
96 L A -1.4067
97 R A -2.2643
98 L A -1.3516
99 R A -1.2963
100 D A -1.8803
101 A A -1.1967
102 W A 0.0000
103 I A -0.2423
104 E A -1.6224
105 H A -0.9731
106 P A -0.7595
107 D A -0.8208
108 H A -0.7945
109 T A -0.5991
110 I A 0.0000
111 L A 0.0000
112 K A 0.0000
113 A A 0.0000
114 L A 0.0000
115 V A 0.0000
116 I A 0.0000
117 E A 0.0000
118 R A -0.7282
119 A A 0.0000
120 I A 0.0000
121 F A 0.0000
122 F A -0.1871
123 V A 0.0000
124 L A 0.0000
125 L A 0.0000
126 P A -0.4295
127 F A 0.0000
128 F A 0.0000
129 R A -0.6387
130 F A 0.0000
131 N A 0.0000
132 G A 0.0000
133 D A 0.0000
134 A A -1.1136
135 G A 0.0000
136 L A 0.0000
137 R A -0.8237
138 T A 0.0000
139 V A 0.0000
140 S A 0.0000
141 A A -0.4748
142 D A 0.0000
143 I A 0.0000
144 S A -0.6587
145 R A -1.6530
146 D A 0.0000
147 E A 0.0000
148 Q A -1.6305
149 I A 0.0000
150 H A 0.0000
151 V A 0.0000
152 A A -0.2216
153 T A 0.0000
154 N A 0.0000
155 S A -0.0028
156 L A 0.1229
157 V A 0.0000
158 C A 0.0000
159 A A -0.6398
160 E A -1.1054
161 L A -0.6293
162 G A -0.7910
163 L A -0.8261
164 K A -1.7735
165 P A -1.2369
166 S A -1.4595
167 Q A -1.9942
168 S A -1.5471
169 L A 0.0000
170 D A -1.6093
171 K A -2.3753
172 L A -1.2403
173 R A 0.0000
174 K A -1.6660
175 A A -1.0089
176 T A 0.0000
177 I A 0.0000
178 N A -1.4458
179 W A -0.9761
180 I A 0.0000
181 M A 0.0000
182 Q A -2.1331
183 P A -1.8512
184 L A 0.0000
185 N A -2.0478
186 Q A -1.5196
187 I A -0.1333
188 H A -1.5231
189 D A -2.2180
190 D A -1.6835
191 Q A -1.4737
192 Y A -0.7258
193 L A 0.0000
194 S A 0.0000
195 K A -1.6526
196 K A -1.5141
197 F A -0.6385
198 W A 0.0000
199 L A -1.0767
200 D A -1.2297
201 A A 0.0000
202 S A 0.0000
203 D A -1.2667
204 R A -1.7087
205 L A 0.0000
206 M A 0.0000
207 Y A -0.1533
208 E A -1.9054
209 G A -1.8740
210 K A -2.6175
211 A A -1.7714
212 P A -1.4519
213 E A -1.5576
214 F A 0.0000
215 N A -2.9016
216 E A -3.0265
217 T A -2.2544
218 K A -2.6824
219 A A -1.4610
220 A A -0.5435
221 R A -0.2612
222 M A 1.0906
223 P A 0.7976
224 A A 1.1773
225 F A 2.2257
226 F A 1.8186
227 E A -0.4807
228 H A -0.0819
229 A A -0.2961
230 N A -0.8698
231 T A -0.8255
232 N A 0.0000
233 L A -0.1736
234 P A -0.5228
235 Q A -1.0353
236 Y A -0.6216
237 S A -0.7802
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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
AR224A -0.6631 -0.0171 View CSV PDB
AD224A -0.6203 -0.0119 View CSV PDB
FR225A 0.106 -0.0468 View CSV PDB
MR222A 0.1055 -0.0252 View CSV PDB
FK225A 0.2214 -0.0462 View CSV PDB
MD222A 0.2104 -0.025 View CSV PDB
FR226A 0.4951 -0.0402 View CSV PDB
FK226A 0.5398 -0.0382 View CSV PDB
PR44A 1.9567 -0.0109 View CSV PDB
PK44A 2.1626 -0.0111 View CSV PDB
PK223A 1.5106 -0.0029 View CSV PDB
PR223A 1.9024 -0.003 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018