Project name: Mihailspm9

Status: done

Started: 2026-05-11 12:14:29
Settings
Chain sequence(s) A: MPLQKIPLKKVEDKYYVGEIEIGTPPQTLYPIFDTGSTDSYFITTLATTPAALKVKRYDPSKSTSYKPYTPATALDLTTPDFVVKGKIAVDTIKIGDFVLKDVAFGAVEEVAPVDDGPNLFDLYPVEGVLGLAFKKLLTYGTKTVLESYFDSYDVPERRFSVYIGDDGSQSALILNGGRDPSYYSGKNWFDVVEDKYWQIKFDGLYLGDKLFFSGSSPEKLKLERYLLIDTGAPFDSVPTEDFDKFLELVPAKPANDSNIDEVIASYPNITYVIDGIPWTLTPEQYLVREGDTAKPAVEKIDIPKELGHVFVAGSTSFLRYFYAEFKFGDENTPSKVGLAKRIDK
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                                          (00:05:26)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 0.669 (methionine) selected    
                       for automated muatation                                                     (00:05:28)
[INFO]       Auto_mut: Residue number 123 from chain A and a score of 0.543 (leucine) selected for 
                       automated muatation                                                         (00:05:28)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 0.385 (leucine) selected for   
                       automated muatation                                                         (00:05:28)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.280 (proline) selected for   
                       automated muatation                                                         (00:05:28)
[INFO]       Auto_mut: Residue number 53 from chain A and a score of 0.124 (leucine) selected for  
                       automated muatation                                                         (00:05:28)
[INFO]       Auto_mut: Residue number 213 from chain A and a score of 0.093 (phenylalanine)        
                       selected for automated muatation                                            (00:05:28)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:05:28)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:05:28)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into glutamic acid       (00:05:28)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:08:26)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:08:31)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into lysine              (00:08:40)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into aspartic acid       (00:11:28)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into glutamic acid         (00:11:32)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into aspartic acid         (00:11:34)
[INFO]       Auto_mut: Mutating residue number 123 from chain A (leucine) into arginine            (00:14:17)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into arginine              (00:14:35)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (leucine) into lysine                (00:14:41)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (proline) into glutamic acid         (00:17:10)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (proline) into aspartic acid         (00:17:26)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (leucine) into glutamic acid        (00:17:48)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (proline) into lysine                (00:20:05)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (proline) into arginine              (00:20:13)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (leucine) into lysine               (00:20:51)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (leucine) into aspartic acid        (00:22:56)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 213 from chain A (phenylalanine) into glutamic acid (00:23:05)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 213 from chain A (phenylalanine) into aspartic acid (00:23:41)
[INFO]       Auto_mut: Mutating residue number 53 from chain A (leucine) into arginine             (00:25:36)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (phenylalanine) into lysine        (00:25:51)
[INFO]       Auto_mut: Mutating residue number 213 from chain A (phenylalanine) into arginine      (00:26:35)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: 1.2677 kcal/mol, Difference in average score from  
                       the base case: -0.0071                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: 0.8462 kcal/mol, Difference in average score from the    
                       base case: -0.0196                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: 1.3792 kcal/mol, Difference in average score from  
                       the base case: -0.0199                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: 0.8674 kcal/mol, Difference in average score   
                       from the base case: -0.0214                                                 (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.9681 kcal/mol, Difference in average score from  
                       the base case: -0.0188                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into lysine:   
                       Energy difference: 0.7802 kcal/mol, Difference in average score from the    
                       base case: -0.0145                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.4953 kcal/mol, Difference in average score from  
                       the base case: -0.0185                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 123 from chain A (leucine) into arginine: 
                       Energy difference: 0.5901 kcal/mol, Difference in average score from the    
                       base case: -0.0188                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into glutamic    
                       acid: Energy difference: 1.4733 kcal/mol, Difference in average score from  
                       the base case: -0.0217                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into lysine:     
                       Energy difference: 0.4673 kcal/mol, Difference in average score from the    
                       base case: -0.0108                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into aspartic    
                       acid: Energy difference: 1.6646 kcal/mol, Difference in average score from  
                       the base case: -0.0183                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (leucine) into arginine:   
                       Energy difference: -0.1110 kcal/mol, Difference in average score from the   
                       base case: -0.0087                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (proline) into glutamic    
                       acid: Energy difference: 0.1541 kcal/mol, Difference in average score from  
                       the base case: 0.0062                                                       (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (proline) into lysine:     
                       Energy difference: 0.0462 kcal/mol, Difference in average score from the    
                       base case: -0.0075                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (proline) into aspartic    
                       acid: Energy difference: 0.0820 kcal/mol, Difference in average score from  
                       the base case: -0.0094                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (proline) into arginine:   
                       Energy difference: 0.0247 kcal/mol, Difference in average score from the    
                       base case: -0.0087                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (leucine) into glutamic   
                       acid: Energy difference: 0.1596 kcal/mol, Difference in average score from  
                       the base case: -0.0142                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (leucine) into lysine:    
                       Energy difference: 0.2051 kcal/mol, Difference in average score from the    
                       base case: -0.0257                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.2714 kcal/mol, Difference in average score from  
                       the base case: -0.0262                                                      (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 53 from chain A (leucine) into arginine:  
                       Energy difference: -0.1445 kcal/mol, Difference in average score from the   
                       base case: -0.0269                                                          (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.3274 kcal/mol, Difference in average    
                       score from the base case: 0.0016                                            (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.4846 kcal/mol, Difference in average score     
                       from the base case: 0.0017                                                  (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.3431 kcal/mol, Difference in average    
                       score from the base case: 0.0079                                            (00:29:20)
[INFO]       Auto_mut: Effect of mutation residue number 213 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.4193 kcal/mol, Difference in average score   
                       from the base case: 0.0020                                                  (00:29:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:28)
Show buried residues
Minimal score value
-3.5195
Maximal score value
0.6695
Average score
-0.8677
Total score value
-299.3558
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 0.6695
2 P A 0.2800
3 L A 0.3854
4 Q A -0.7748
5 K A -1.4223
6 I A 0.0000
7 P A -1.4554
8 L A 0.0000
9 K A -3.0126
10 K A -3.4341
11 V A 0.0000
12 E A -3.0357
13 D A -3.5195
14 K A -1.9708
15 Y A -1.4851
16 Y A 0.0000
17 V A 0.0000
18 G A 0.0000
19 E A -1.2330
20 I A 0.0000
21 E A -0.8542
22 I A 0.0000
23 G A 0.0000
24 T A -0.6730
25 P A -0.8033
26 P A -0.7962
27 Q A -1.0158
28 T A -0.7812
29 L A 0.0000
30 Y A -0.5734
31 P A 0.0000
32 I A 0.0000
33 F A 0.0000
34 D A -0.2792
35 T A 0.0000
36 G A -0.2599
37 S A -0.2188
38 T A 0.0000
39 D A 0.0000
40 S A 0.0000
41 Y A 0.0000
42 F A 0.0000
43 I A 0.0000
44 T A 0.0000
45 T A -0.3601
46 L A -0.3267
47 A A 0.0000
48 T A -0.3306
49 T A -0.4350
50 P A -0.2518
51 A A 0.0000
52 A A 0.0000
53 L A 0.1242
54 K A -1.3445
55 V A -1.0633
56 K A -1.6965
57 R A -1.1297
58 Y A 0.0000
59 D A -1.0928
60 P A -0.9949
61 S A -1.1410
62 K A -2.0050
63 S A -1.2662
64 T A -0.7377
65 S A -1.1309
66 Y A -1.1020
67 K A -1.5466
68 P A -0.9055
69 Y A -0.6386
70 T A -0.3523
71 P A -0.2599
72 A A -0.2165
73 T A -0.4879
74 A A -0.8822
75 L A 0.0000
76 D A -2.1445
77 L A -0.7432
78 T A -0.4773
79 T A -0.6160
80 P A -1.2979
81 D A -1.8951
82 F A 0.0000
83 V A -0.6436
84 V A 0.0000
85 K A -2.3919
86 G A -2.0743
87 K A -1.5804
88 I A 0.0000
89 A A 0.0000
90 V A 0.0000
91 D A 0.0000
92 T A 0.0000
93 I A 0.0000
94 K A -1.0559
95 I A 0.0000
96 G A -1.7530
97 D A -1.9158
98 F A 0.0000
99 V A -0.3370
100 L A 0.0000
101 K A -2.4541
102 D A -2.7695
103 V A 0.0000
104 A A -0.9958
105 F A 0.0000
106 G A 0.0000
107 A A 0.0000
108 V A 0.0000
109 E A -2.4117
110 E A -2.0902
111 V A 0.0000
112 A A -0.8082
113 P A -1.0658
114 V A -0.4951
115 D A -2.4282
116 D A -2.5814
117 G A -1.8931
118 P A -1.0463
119 N A 0.0000
120 L A 0.0000
121 F A 0.0000
122 D A -0.1651
123 L A 0.5435
124 Y A -0.1374
125 P A -0.5684
126 V A 0.0000
127 E A -0.7206
128 G A 0.0000
129 V A 0.0000
130 L A 0.0000
131 G A 0.0000
132 L A 0.0000
133 A A 0.0000
134 F A 0.0000
135 K A -2.1681
136 K A -2.4316
137 L A -0.8996
138 L A -0.7943
139 T A -0.2562
140 Y A 0.0000
141 G A -0.7084
142 T A -0.8048
143 K A -1.6370
144 T A 0.0000
145 V A 0.0000
146 L A 0.0000
147 E A -1.4772
148 S A -1.4850
149 Y A 0.0000
150 F A -1.5272
151 D A -2.3806
152 S A -1.4375
153 Y A -0.9956
154 D A -2.0504
155 V A -1.3093
156 P A -1.1719
157 E A -1.6239
158 R A -2.0120
159 R A -1.1682
160 F A 0.0000
161 S A 0.0000
162 V A 0.0000
163 Y A 0.0000
164 I A 0.0000
165 G A 0.0000
166 D A -3.3961
167 D A -3.4897
168 G A 0.0000
169 S A -1.9729
170 Q A -2.2555
171 S A 0.0000
172 A A 0.0000
173 L A 0.0000
174 I A 0.0000
175 L A 0.0000
176 N A 0.0000
177 G A -0.4850
178 G A 0.0000
179 R A -1.1113
180 D A -0.8263
181 P A -0.6193
182 S A -0.7275
183 Y A 0.0000
184 Y A -0.9066
185 S A -0.8919
186 G A -1.2448
187 K A -1.0883
188 N A -0.8308
189 W A -0.5406
190 F A 0.0000
191 D A -2.1336
192 V A 0.0000
193 V A -1.1933
194 E A -2.3235
195 D A -1.9635
196 K A -1.7930
197 Y A -0.8379
198 W A 0.0000
199 Q A 0.0000
200 I A 0.0000
201 K A -2.6564
202 F A 0.0000
203 D A -2.6435
204 G A 0.0000
205 L A 0.0000
206 Y A -0.6293
207 L A 0.0000
208 G A -1.5451
209 D A -2.4178
210 K A -1.8325
211 L A -0.4186
212 F A 0.0000
213 F A 0.0930
214 S A -0.8860
215 G A -1.0498
216 S A -0.7006
217 S A -1.2505
218 P A -1.5116
219 E A -2.5962
220 K A -2.0706
221 L A -0.8967
222 K A -2.2999
223 L A -1.6904
224 E A -2.4191
225 R A 0.0000
226 Y A -1.0064
227 L A 0.0000
228 L A 0.0000
229 I A 0.0000
230 D A -0.2407
231 T A 0.0000
232 G A -0.2479
233 A A 0.0000
234 P A -0.4985
235 F A -0.3414
236 D A 0.0000
237 S A 0.0000
238 V A 0.0000
239 P A 0.0000
240 T A -2.1356
241 E A -2.4405
242 D A 0.0000
243 F A -1.9569
244 D A -2.8189
245 K A -2.1263
246 F A 0.0000
247 L A -1.1907
248 E A -2.0463
249 L A -0.5932
250 V A 0.0000
251 P A -0.8807
252 A A -0.7117
253 K A -1.1402
254 P A -1.6257
255 A A 0.0000
256 N A -3.0283
257 D A -2.7522
258 S A -1.9074
259 N A -2.0997
260 I A -2.3896
261 D A -3.1004
262 E A -2.6192
263 V A 0.0000
264 I A -1.4021
265 A A -1.2955
266 S A -0.8809
267 Y A 0.0000
268 P A -0.7107
269 N A -1.1762
270 I A 0.0000
271 T A -0.3573
272 Y A 0.0000
273 V A -0.8745
274 I A 0.0000
275 D A -2.4745
276 G A -1.3485
277 I A -0.3986
278 P A -0.3462
279 W A 0.0000
280 T A -0.1328
281 L A 0.0000
282 T A -0.9232
283 P A 0.0000
284 E A -2.0901
285 Q A -1.1732
286 Y A 0.0000
287 L A -0.8728
288 V A -1.0890
289 R A -2.6794
290 E A -3.2382
291 G A -2.6669
292 D A -3.3651
293 T A -2.4117
294 A A 0.0000
295 K A -1.1216
296 P A 0.0000
297 A A 0.0000
298 V A 0.0000
299 E A -1.8881
300 K A -2.7385
301 I A -1.4127
302 D A -2.2396
303 I A -1.3762
304 P A -1.7292
305 K A -2.8341
306 E A -2.6322
307 L A -1.5011
308 G A -1.5127
309 H A 0.0000
310 V A 0.0000
311 F A 0.0000
312 V A 0.0000
313 A A 0.0000
314 G A 0.0000
315 S A 0.0000
316 T A 0.0000
317 S A 0.0000
318 F A 0.0000
319 L A 0.0000
320 R A -0.9978
321 Y A -0.7612
322 F A 0.0000
323 Y A 0.0000
324 A A 0.0000
325 E A 0.0000
326 F A 0.0000
327 K A -1.1802
328 F A -1.0225
329 G A -2.1991
330 D A -3.2252
331 E A -3.3396
332 N A -2.7778
333 T A -2.0775
334 P A -2.0022
335 S A 0.0000
336 K A -1.2964
337 V A 0.0000
338 G A 0.0000
339 L A 0.0000
340 A A 0.0000
341 K A -1.9602
342 R A 0.0000
343 I A -0.9947
344 D A -2.7781
345 K A -2.7090
Download PDB file
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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
LR53A -0.1445 -0.0269 View CSV PDB
LR3A -0.111 -0.0087 View CSV PDB
PR2A 0.0247 -0.0087 View CSV PDB
PK2A 0.0462 -0.0075 View CSV PDB
LK53A 0.2051 -0.0257 View CSV PDB
LR123A 0.5901 -0.0188 View CSV PDB
MR1A 0.8674 -0.0214 View CSV PDB
MK1A 0.8462 -0.0196 View CSV PDB
LK3A 0.4673 -0.0108 View CSV PDB
LE123A 0.9681 -0.0188 View CSV PDB
FK213A 1.4846 0.0017 View CSV PDB
FR213A 1.4193 0.002 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018