Project name: ddb27c5db5235ab

Status: done

Started: 2026-06-15 07:31:17
Chain sequence(s) A: VYTHDTGLDYITYSDYELDPANPLAGGAAWIEGAFVPPSEARISIFDQGFYTSDATYTTFHVWNGNAFRLGDHIERLFSNAESIRLIPPLTQDEVKEIALELVAKTELREAMVTVTITRGYSSTPFERDITKHRPQVYMSAPYQWIVPFDRIRDGVHLMVAQSVRRTPRSSIDPQVKNFQWGDLIRAIQETHDRGFELPLLLDCDNLLAEGPGFNVVVIKDGVVRSPGRAALPGITRKTVLEIAESLGHEAILADITPAELYDADEVLGCSTGGGVWPFVSVDGNSISDGVPGPVTQSIIRRYWELNVEPSSLLTPVQY
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:38)
[INFO]       AutoMut:  Residue number 56 from chain A and a score of 3.841 (phenylalanine)         
                       selected for automated mutation                                             (00:02:40)
[INFO]       AutoMut:  Residue number 55 from chain A and a score of 3.680 (isoleucine) selected   
                       for automated mutation                                                      (00:02:40)
[INFO]       AutoMut:  Residue number 60 from chain A and a score of 3.435 (phenylalanine)         
                       selected for automated mutation                                             (00:02:40)
[INFO]       AutoMut:  Residue number 61 from chain A and a score of 2.524 (tyrosine) selected for 
                       automated mutation                                                          (00:02:40)
[INFO]       AutoMut:  Residue number 54 from chain A and a score of 2.172 (serine) selected for   
                       automated mutation                                                          (00:02:40)
[INFO]       AutoMut:  Residue number 11 from chain A and a score of 1.625 (valine) selected for   
                       automated mutation                                                          (00:02:40)
[INFO]       AutoMut:  Mutating residue number 56 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 56 from chain A (phenylalanine) into glutamic acid  (00:02:40)
[INFO]       AutoMut:  Mutating residue number 56 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 56 from chain A (phenylalanine) into aspartic acid  (00:02:40)
[INFO]       AutoMut:  Mutating residue number 55 from chain A (isoleucine) into glutamic acid     (00:02:40)
[INFO]       AutoMut:  Mutating residue number 56 from chain A (phenylalanine) into arginine       (00:02:50)
[INFO]       AutoMut:  Mutating residue number 55 from chain A (isoleucine) into lysine            (00:02:50)
[INFO]       AutoMut:  Mutating residue number 56 from chain A (phenylalanine) into lysine         (00:02:55)
[INFO]       AutoMut:  Mutating residue number 55 from chain A (isoleucine) into aspartic acid     (00:03:02)
[INFO]       AutoMut:  Mutating residue number 55 from chain A (isoleucine) into arginine          (00:03:11)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 60 from chain A (phenylalanine) into glutamic acid  (00:03:12)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 60 from chain A (phenylalanine) into aspartic acid  (00:03:15)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (phenylalanine) into arginine       (00:03:24)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (phenylalanine) into lysine         (00:03:25)
[INFO]       AutoMut:  Mutating residue number 61 from chain A (tyrosine) into glutamic acid       (00:03:27)
[INFO]       AutoMut:  Mutating residue number 61 from chain A (tyrosine) into aspartic acid       (00:03:41)
[INFO]       AutoMut:  Mutating residue number 61 from chain A (tyrosine) into lysine              (00:03:43)
[INFO]       AutoMut:  Mutating residue number 54 from chain A (serine) into glutamic acid         (00:03:47)
[INFO]       AutoMut:  Mutating residue number 61 from chain A (tyrosine) into arginine            (00:03:53)
[INFO]       AutoMut:  Mutating residue number 54 from chain A (serine) into lysine                (00:03:58)
[INFO]       AutoMut:  Mutating residue number 54 from chain A (serine) into aspartic acid         (00:04:11)
[INFO]       AutoMut:  Mutating residue number 11 from chain A (valine) into glutamic acid         (00:04:13)
[INFO]       AutoMut:  Mutating residue number 11 from chain A (valine) into aspartic acid         (00:04:21)
[INFO]       AutoMut:  Mutating residue number 11 from chain A (valine) into lysine                (00:04:21)
[INFO]       AutoMut:  Mutating residue number 54 from chain A (serine) into arginine              (00:04:23)
[INFO]       AutoMut:  Mutating residue number 11 from chain A (valine) into arginine              (00:04:28)
[INFO]       AutoMut:  Effect of mutation residue number 56 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.1103 kcal/mol, Difference in average    
                       score from the base case: -0.0364                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 56 from chain A (phenylalanine) into      
                       lysine: Energy difference: 0.0584 kcal/mol, Difference in average score     
                       from the base case: -0.0351                                                 (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 56 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.4549 kcal/mol, Difference in average    
                       score from the base case: -0.0359                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 56 from chain A (phenylalanine) into      
                       arginine: Energy difference: -0.9806 kcal/mol, Difference in average score  
                       from the base case: -0.0413                                                 (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 55 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.4675 kcal/mol, Difference in average   
                       score from the base case: -0.0339                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 55 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.2704 kcal/mol, Difference in average score from the   
                       base case: -0.0328                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 55 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 0.0307 kcal/mol, Difference in average    
                       score from the base case: -0.0339                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 55 from chain A (isoleucine) into         
                       arginine: Energy difference: -1.2794 kcal/mol, Difference in average score  
                       from the base case: -0.0436                                                 (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: 0.2348 kcal/mol, Difference in average    
                       score from the base case: -0.0422                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (phenylalanine) into      
                       lysine: Energy difference: -0.1069 kcal/mol, Difference in average score    
                       from the base case: -0.0417                                                 (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: 0.6067 kcal/mol, Difference in average    
                       score from the base case: -0.0391                                           (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (phenylalanine) into      
                       arginine: Energy difference: -0.1017 kcal/mol, Difference in average score  
                       from the base case: -0.0402                                                 (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 61 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 0.9838 kcal/mol, Difference in average score from  
                       the base case: -0.0247                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 61 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.4151 kcal/mol, Difference in average score from the    
                       base case: -0.0231                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 61 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.1323 kcal/mol, Difference in average score from  
                       the base case: -0.0244                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 61 from chain A (tyrosine) into arginine: 
                       Energy difference: 0.3196 kcal/mol, Difference in average score from the    
                       base case: -0.0197                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 54 from chain A (serine) into glutamic    
                       acid: Energy difference: -0.5323 kcal/mol, Difference in average score from 
                       the base case: -0.0138                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 54 from chain A (serine) into lysine:     
                       Energy difference: -0.8682 kcal/mol, Difference in average score from the   
                       base case: -0.0152                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 54 from chain A (serine) into aspartic    
                       acid: Energy difference: 0.0259 kcal/mol, Difference in average score from  
                       the base case: -0.0089                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 54 from chain A (serine) into arginine:   
                       Energy difference: -2.5811 kcal/mol, Difference in average score from the   
                       base case: -0.0218                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 11 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.0709 kcal/mol, Difference in average score from  
                       the base case: -0.0261                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 11 from chain A (valine) into lysine:     
                       Energy difference: -0.3503 kcal/mol, Difference in average score from the   
                       base case: -0.0240                                                          (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 11 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.0379 kcal/mol, Difference in average score from 
                       the base case: -0.0274                                                      (00:04:45)
[INFO]       AutoMut:  Effect of mutation residue number 11 from chain A (valine) into arginine:   
                       Energy difference: -0.8186 kcal/mol, Difference in average score from the   
                       base case: -0.0251                                                          (00:04:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:53)
Show buried residues
Minimal score value
-3.3686
Maximal score value
3.8413
Average score
-0.5733
Total score value
-182.8947
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
11 V A 1.6251
12 Y A 0.3608
13 T A -0.3768
14 H A -1.0406
15 D A -2.3033
16 T A -1.9507
17 G A -1.9325
18 L A -1.7999
19 D A -2.0414
20 Y A -1.1543
21 I A 0.0000
22 T A -0.9410
23 Y A -0.9470
24 S A -1.3633
25 D A -2.1961
26 Y A -1.7516
27 E A -2.3288
28 L A -1.3596
29 D A -1.9448
30 P A -1.1898
31 A A -0.6852
32 N A -1.0373
33 P A -0.8062
34 L A 0.0000
35 A A -1.0326
36 G A -0.5073
37 G A -0.4276
38 A A 0.0000
39 A A 0.0000
40 W A -0.4362
41 I A -1.0235
42 E A -1.7630
43 G A -1.0961
44 A A -0.4169
45 F A -0.2580
46 V A 0.0000
47 P A -1.1569
48 P A -1.3071
49 S A -1.5765
50 E A -2.4150
51 A A -1.6191
52 R A -1.7711
53 I A 0.6337
54 S A 2.1723
55 I A 3.6796
56 F A 3.8413
57 D A 0.0000
58 Q A 0.0000
59 G A 0.0000
60 F A 3.4351
61 Y A 2.5244
62 T A 1.0421
63 S A 0.8908
64 D A 0.3267
65 A A 0.0000
66 T A 0.0000
67 Y A 0.0959
68 T A 0.0000
69 T A -0.0243
70 F A 0.0000
71 H A 0.0000
72 V A 0.0000
73 W A 0.0000
74 N A -0.9643
75 G A 0.0000
76 N A -0.6065
77 A A 0.0000
78 F A 0.0000
79 R A -0.4192
80 L A 0.0000
81 G A -1.7335
82 D A -1.6728
83 H A 0.0000
84 I A 0.0000
85 E A -2.5903
86 R A -1.8828
87 L A 0.0000
88 F A 0.0000
89 S A -1.1219
90 N A 0.0000
91 A A 0.0000
92 E A -1.1589
93 S A -0.8120
94 I A -0.5022
95 R A -1.5224
96 L A 0.0000
97 I A 0.9459
98 P A 0.0000
99 P A -0.2273
100 L A -0.4346
101 T A -1.1200
102 Q A -2.6767
103 D A -3.2484
104 E A -2.7292
105 V A 0.0000
106 K A -2.5354
107 E A -3.2302
108 I A -1.6644
109 A A 0.0000
110 L A 0.0000
111 E A -1.5870
112 L A 0.0000
113 V A 0.0000
114 A A -0.7047
115 K A -1.0381
116 T A 0.0000
117 E A -1.1047
118 L A 0.0000
119 R A -0.9715
120 E A 0.0000
121 A A 0.0000
122 M A -0.2468
123 V A 0.0000
124 T A -0.0030
125 V A 0.0000
126 T A 0.0883
127 I A 0.0000
128 T A 0.0000
129 R A -0.4096
130 G A 0.0000
131 Y A 1.3443
132 S A -0.5703
133 S A -0.3931
134 T A 0.1491
135 P A 0.3183
136 F A 0.9431
137 E A -0.7595
138 R A -1.5652
139 D A -0.7623
140 I A 0.3903
141 T A -0.6534
142 K A -2.0740
143 H A -1.4923
144 R A -1.9090
145 P A -0.8203
146 Q A -0.7579
147 V A 0.0000
148 Y A 0.0000
149 M A 0.0000
150 S A -0.0412
151 A A -0.2642
153 P A 0.0194
154 Y A 0.0000
155 Q A -0.7682
156 W A -0.1121
157 I A 0.3878
158 V A 0.0000
159 P A -1.1780
160 F A -1.8133
161 D A -2.9730
162 R A -2.4535
163 I A 0.0000
164 R A -3.1172
165 D A -2.1942
166 G A 0.0000
167 V A 0.0000
168 H A -0.8916
169 L A 0.0000
170 M A 0.0000
171 V A 0.0000
172 A A 0.0000
173 Q A -1.3590
174 S A -1.0486
175 V A -0.8407
176 R A -1.1915
177 R A 0.0000
178 T A -0.4394
179 P A -0.9197
180 R A -1.7914
181 S A -0.8414
182 S A -0.4114
183 I A 0.1575
184 D A -0.7322
185 P A 0.0000
186 Q A -0.8198
187 V A -0.1003
188 K A -0.3005
189 N A 0.2257
190 F A 0.9457
191 Q A 0.1488
192 W A 0.1530
193 G A -0.3494
194 D A -0.5536
195 L A 0.0000
196 I A 0.3756
197 R A -1.1668
198 A A 0.0000
199 I A -0.4564
200 Q A -1.7466
201 E A 0.0000
202 T A 0.0000
203 H A -2.8754
204 D A -3.3686
205 R A -3.3216
206 G A -2.3045
207 F A -1.5123
208 E A -1.1245
209 L A -0.2288
210 P A 0.0000
211 L A 0.0000
212 L A 0.0000
213 L A 0.0000
214 D A 0.0000
215 C A -0.7786
216 D A -1.9479
217 N A -1.7868
218 L A -1.2807
219 L A 0.0000
220 A A 0.0000
221 E A 0.0000
222 G A 0.0000
223 P A 0.1991
224 G A -0.0563
225 F A 0.0000
226 N A 0.0000
227 V A 0.0000
228 V A 0.0000
229 V A 0.0000
230 I A 0.0000
231 K A -2.0650
232 D A -2.4010
233 G A -1.6448
234 V A -1.2646
235 V A 0.0000
236 R A -0.1000
237 S A 0.0000
238 P A 0.0000
239 G A -1.1759
240 R A -2.3511
241 A A 0.0000
242 A A 0.0000
243 L A -0.3220
244 P A -0.5942
245 G A -0.3512
246 I A -0.4350
247 T A 0.0000
248 R A -0.5446
249 K A -0.8394
250 T A 0.0000
251 V A 0.0000
252 L A 0.0000
253 E A -1.6392
254 I A 0.0000
255 A A 0.0000
256 E A -2.5469
257 S A -1.4623
258 L A -0.8022
259 G A -1.3392
260 H A -1.9209
261 E A -2.4153
262 A A -0.9844
263 I A 0.4536
264 L A 0.3984
265 A A -0.3998
266 D A -1.4558
267 I A 0.0000
268 T A -0.7254
269 P A -0.4686
270 A A -0.5188
271 E A -1.2436
272 L A 0.0000
273 Y A -1.0756
274 D A -2.1821
275 A A 0.0000
276 D A -2.0700
277 E A 0.0000
278 V A 0.0000
279 L A 0.0000
280 G A 0.0000
281 C A 0.0000
282 S A 0.0109
283 T A -0.1040
284 G A -0.1515
285 G A 0.0000
286 G A 0.0000
287 V A 0.0000
288 W A 0.0000
289 P A 0.0000
290 F A 0.0000
291 V A -0.1371
292 S A 0.0000
293 V A 0.0000
294 D A -1.1685
295 G A -1.1830
296 N A -1.4984
297 S A -1.2789
298 I A 0.0000
299 S A -1.4241
300 D A -1.5365
301 G A -0.5057
302 V A 0.5365
303 P A -0.3837
304 G A -0.4297
305 P A -0.4317
306 V A -0.4102
307 T A 0.0000
308 Q A -1.6466
309 S A -1.0369
310 I A 0.0000
311 I A 0.0000
312 R A -1.9285
313 R A -1.7296
314 Y A 0.0000
315 W A 0.0000
316 E A -1.6790
317 L A -0.9843
318 N A 0.0000
319 V A -0.4239
320 E A -1.8008
321 P A -1.0322
322 S A -0.5116
323 S A -0.3791
324 L A -0.1617
325 L A -0.2628
326 T A -0.4451
327 P A -0.5916
328 V A 0.0000
329 Q A -1.2545
330 Y A 0.2546
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

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
IR55A -1.2794 -0.0436 View CSV PDB
SR54A -2.5811 -0.0218 View CSV PDB
FR56A -0.9806 -0.0413 View CSV PDB
VR11A -0.8186 -0.0251 View CSV PDB
IE55A -0.4675 -0.0339 View CSV PDB
FK60A -0.1069 -0.0417 View CSV PDB
FR60A -0.1017 -0.0402 View CSV PDB
SK54A -0.8682 -0.0152 View CSV PDB
VK11A -0.3503 -0.024 View CSV PDB
FK56A 0.0584 -0.0351 View CSV PDB
YR61A 0.3196 -0.0197 View CSV PDB
YK61A 0.4151 -0.0231 View CSV PDB