Project name: ALAS

Status: done

Started: 2026-03-05 07:47:13
Settings
Chain sequence(s) A: MDYTKFFADALDRLHAERRYRVFADLERVAGRFPHATWHSPSGERDVVIWCSNDYLGMGQHPKVVGAMVETATRLGTGAGGTRNIAGTHHPLVMLERELADLHGKEAALLFTSGYVSNQTGISTLAKLIPNCLILSDALNHNSMIEGIRQSGCERIVWRHNDTAHLEELLRAVEPGRPVLIAFESLYSMDGDVAPMAKICDLAEKYGAMTYCDEVHAVGMYGARGAGVAERDGVMHRIDIIEATLAKAFGCLGGYISGKKDVIDAVRSYAPGFIFTTALPPPICAAATAAIRHLKTSTWERERHQDRAARLKAVLNTAGLPVMPTDTHIVPVFVGDAERCKKASDLLLEKHGIYIQPINYPTVAKGKERLRITPSPYHDDDLMDRLAEALVDVWETLELPLGAKPLAAE
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                                          (00:08:27)
[INFO]       Auto_mut: Residue number 22 from chain A and a score of 2.155 (valine) selected for   
                       automated muatation                                                         (00:08:30)
[INFO]       Auto_mut: Residue number 23 from chain A and a score of 2.105 omitted from automated  
                       muatation (excluded by the user).                                           (00:08:30)
[INFO]       Auto_mut: Residue number 275 from chain A and a score of 1.742 omitted from automated 
                       muatation (excluded by the user).                                           (00:08:30)
[INFO]       Auto_mut: Residue number 7 from chain A and a score of 1.699 (phenylalanine) selected 
                       for automated muatation                                                     (00:08:30)
[INFO]       Auto_mut: Residue number 6 from chain A and a score of 1.653 (phenylalanine) selected 
                       for automated muatation                                                     (00:08:30)
[INFO]       Auto_mut: Residue number 85 from chain A and a score of 1.279 omitted from automated  
                       muatation (excluded by the user).                                           (00:08:30)
[INFO]       Auto_mut: Residue number 274 from chain A and a score of 1.054 omitted from automated 
                       muatation (excluded by the user).                                           (00:08:30)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 1.045 omitted from automated   
                       muatation (excluded by the user).                                           (00:08:30)
[INFO]       Auto_mut: Residue number 252 from chain A and a score of 0.848 (leucine) selected for 
                       automated muatation                                                         (00:08:30)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (valine) into glutamic acid         (00:08:30)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (valine) into aspartic acid         (00:08:30)
[INFO]       Auto_mut: Mutating residue number 7 from chain A (phenylalanine) into glutamic acid   (00:08:30)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (valine) into arginine              (00:11:54)
[INFO]       Auto_mut: Mutating residue number 7 from chain A (phenylalanine) into lysine          (00:12:03)
[INFO]       Auto_mut: Mutating residue number 22 from chain A (valine) into lysine                (00:12:24)
[INFO]       Auto_mut: Mutating residue number 7 from chain A (phenylalanine) into aspartic acid   (00:15:39)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into glutamic acid   (00:16:04)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into aspartic acid   (00:16:31)
[INFO]       Auto_mut: Mutating residue number 7 from chain A (phenylalanine) into arginine        (00:19:37)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into lysine          (00:20:01)
[INFO]       Auto_mut: Mutating residue number 6 from chain A (phenylalanine) into arginine        (00:20:23)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (leucine) into glutamic acid       (00:22:49)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (leucine) into aspartic acid       (00:23:31)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (leucine) into lysine              (00:25:42)
[INFO]       Auto_mut: Mutating residue number 252 from chain A (leucine) into arginine            (00:26:10)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.5304 kcal/mol, Difference in average score from 
                       the base case: -0.0257                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (valine) into lysine:     
                       Energy difference: -0.6239 kcal/mol, Difference in average score from the   
                       base case: -0.0221                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (valine) into aspartic    
                       acid: Energy difference: -0.7361 kcal/mol, Difference in average score from 
                       the base case: -0.0248                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 22 from chain A (valine) into arginine:   
                       Energy difference: -0.6090 kcal/mol, Difference in average score from the   
                       base case: -0.0222                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 7 from chain A (phenylalanine) into       
                       glutamic acid: Energy difference: 0.4451 kcal/mol, Difference in average    
                       score from the base case: -0.0378                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 7 from chain A (phenylalanine) into       
                       lysine: Energy difference: 0.1202 kcal/mol, Difference in average score     
                       from the base case: -0.0393                                                 (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 7 from chain A (phenylalanine) into       
                       aspartic acid: Energy difference: 0.8379 kcal/mol, Difference in average    
                       score from the base case: -0.0420                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 7 from chain A (phenylalanine) into       
                       arginine: Energy difference: 0.2189 kcal/mol, Difference in average score   
                       from the base case: -0.0378                                                 (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       glutamic acid: Energy difference: -0.0682 kcal/mol, Difference in average   
                       score from the base case: -0.0406                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       lysine: Energy difference: 0.2770 kcal/mol, Difference in average score     
                       from the base case: -0.0401                                                 (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       aspartic acid: Energy difference: 0.4678 kcal/mol, Difference in average    
                       score from the base case: -0.0418                                           (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 6 from chain A (phenylalanine) into       
                       arginine: Energy difference: -0.4646 kcal/mol, Difference in average score  
                       from the base case: -0.0395                                                 (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5364 kcal/mol, Difference in average score from  
                       the base case: -0.0181                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (leucine) into lysine:   
                       Energy difference: -0.3016 kcal/mol, Difference in average score from the   
                       base case: -0.0224                                                          (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4995 kcal/mol, Difference in average score from  
                       the base case: -0.0197                                                      (00:28:36)
[INFO]       Auto_mut: Effect of mutation residue number 252 from chain A (leucine) into arginine: 
                       Energy difference: -0.3787 kcal/mol, Difference in average score from the   
                       base case: -0.0234                                                          (00:28:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:28:41)
Show buried residues
Minimal score value
-3.8717
Maximal score value
2.1555
Average score
-0.7131
Total score value
-291.6582
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 0.4761
2 D A -0.6493
3 Y A 1.0450
4 T A 0.3840
5 K A -0.3502
6 F A 1.6528
7 F A 1.6991
8 A A 0.1756
9 D A -0.9314
10 A A -0.4034
11 L A -0.8398
12 D A -2.9242
13 R A -3.2721
14 L A -2.4780
15 H A -3.1239
16 A A -2.7173
17 E A -3.4068
18 R A -3.8558
19 R A -2.0579
20 Y A -0.8927
21 R A 0.1884
22 V A 2.1555
23 F A 2.1053
24 A A 0.1907
25 D A -1.8123
26 L A -1.8940
27 E A -2.7617
28 R A -2.0442
29 V A -1.0756
30 A A -0.9186
31 G A -1.3578
32 R A -1.9934
33 F A 0.0000
34 P A 0.0000
35 H A -1.4722
36 A A 0.0000
37 T A -2.5469
38 W A 0.0000
39 H A -2.8192
40 S A -1.8962
41 P A -1.0657
42 S A -1.0378
43 G A -1.6671
44 E A -3.3864
45 R A -2.9735
46 D A -2.9065
47 V A 0.0000
48 V A 0.0000
49 I A 0.0000
50 W A 0.0000
51 C A -0.0755
52 S A -0.2621
53 N A -0.5612
54 D A 0.0000
55 Y A 0.0000
56 L A 0.0000
57 G A 0.0000
58 M A 0.0000
59 G A -0.3756
60 Q A -0.7772
61 H A -0.8118
62 P A -1.0277
63 K A -1.9179
64 V A 0.0000
65 V A 0.1715
66 G A -0.4903
67 A A -0.3305
68 M A 0.4919
69 V A 0.5470
70 E A -1.3716
71 T A -0.6815
72 A A -0.4259
73 T A -0.9482
74 R A -1.7604
75 L A -0.4302
76 G A -0.5463
77 T A -0.2481
78 G A -0.5534
79 A A -0.2703
80 G A -0.4376
81 G A 0.1832
82 T A 0.5415
83 R A -0.1250
84 N A -0.1400
85 I A 1.2793
86 A A 0.4686
87 G A 0.0000
88 T A -0.3244
89 H A -0.4860
90 H A -0.8671
91 P A -0.3605
92 L A 0.0000
93 V A -0.3535
94 M A -0.4889
95 L A 0.0000
96 E A 0.0000
97 R A -2.4175
98 E A -1.8463
99 L A 0.0000
100 A A 0.0000
101 D A -2.6583
102 L A 0.0000
103 H A 0.0000
104 G A -1.7697
105 K A -2.9042
106 E A -3.7997
107 A A -2.9536
108 A A 0.0000
109 L A 0.0000
110 L A 0.0000
111 F A 0.0000
112 T A 0.2106
113 S A 0.3785
114 G A 0.3916
115 Y A 0.3700
116 V A 0.3715
117 S A 0.0000
118 N A 0.0000
119 Q A -0.5718
120 T A 0.0000
121 G A 0.0000
122 I A 0.0000
123 S A 0.0000
124 T A 0.0000
125 L A 0.0000
126 A A 0.0000
127 K A -1.4850
128 L A 0.1259
129 I A -0.2875
130 P A -0.9080
131 N A -1.8042
132 C A 0.0000
133 L A 0.0000
134 I A 0.0000
135 L A 0.0000
136 S A 0.0000
137 D A 0.0000
138 A A 0.2185
139 L A 0.6536
140 N A 0.0000
141 H A -0.7533
142 N A -1.1143
143 S A 0.0000
144 M A 0.0000
145 I A -0.8696
146 E A -1.4017
147 G A 0.0000
148 I A 0.0000
149 R A -2.8878
150 Q A -2.2571
151 S A 0.0000
152 G A -2.1359
153 C A -2.3592
154 E A -2.7195
155 R A -2.0321
156 I A -0.1383
157 V A 0.5217
158 W A 0.0000
159 R A -1.6759
160 H A -0.8194
161 N A -0.9931
162 D A -1.2257
163 T A -1.2601
164 A A -1.1824
165 H A -1.6849
166 L A 0.0000
167 E A -2.1320
168 E A -2.5846
169 L A -1.1750
170 L A 0.0000
171 R A -2.6841
172 A A -1.6283
173 V A -1.5491
174 E A -2.3398
175 P A -1.6419
176 G A -1.2312
177 R A -1.5378
178 P A -0.8871
179 V A 0.0000
180 L A 0.0000
181 I A 0.0000
182 A A 0.0000
183 F A 0.0000
184 E A 0.0000
185 S A 0.0000
186 L A 0.0000
187 Y A 0.0000
188 S A -0.3550
189 M A -0.3573
190 D A -1.2164
191 G A 0.0000
192 D A -1.6831
193 V A -0.6768
194 A A 0.0000
195 P A -0.7379
196 M A 0.0000
197 A A -1.3532
198 K A -2.1739
199 I A 0.0000
200 C A 0.0000
201 D A -3.2029
202 L A 0.0000
203 A A 0.0000
204 E A -3.3844
205 K A -3.0284
206 Y A -1.8989
207 G A -1.6975
208 A A -0.9950
209 M A -0.5089
210 T A 0.0000
211 Y A 0.0000
212 C A 0.0000
213 D A 0.0000
214 E A 0.0000
215 V A 0.1392
216 H A -0.1299
217 A A 0.0000
218 V A 0.0000
219 G A 0.0000
220 M A 0.0000
221 Y A 0.0000
222 G A -1.1209
223 A A -0.6389
224 R A -1.1904
225 G A 0.0000
226 A A 0.0000
227 G A 0.0000
228 V A 0.0000
229 A A 0.0000
230 E A -1.5735
231 R A -1.9497
232 D A -1.9321
233 G A -1.6097
234 V A 0.0000
235 M A -1.3055
236 H A -1.5571
237 R A -1.5927
238 I A 0.0000
239 D A -1.6403
240 I A 0.0000
241 I A 0.0000
242 E A 0.0000
243 A A 0.0000
244 T A 0.0000
245 L A 0.0000
246 A A 0.1703
247 K A -0.2941
248 A A 0.0000
249 F A 0.0000
250 G A -0.0372
251 C A 0.5521
252 L A 0.8475
253 G A 0.0000
254 G A 0.0000
255 Y A 0.0000
256 I A 0.0000
257 S A 0.0000
258 G A 0.0000
259 K A -3.8090
260 K A -3.8717
261 D A -3.3945
262 V A -2.0640
263 I A 0.0000
264 D A -2.0395
265 A A -0.7413
266 V A 0.0000
267 R A -0.9235
268 S A -0.0100
269 Y A 0.8210
270 A A 0.0000
271 P A 0.5663
272 G A 0.4366
273 F A 0.0000
274 I A 1.0540
275 F A 1.7425
276 T A 0.7051
277 T A 0.2275
278 A A 0.0251
279 L A 0.0000
280 P A -0.0425
281 P A 0.0000
282 P A 0.0000
283 I A 0.8180
284 C A 0.0000
285 A A 0.1379
286 A A 0.0000
287 A A 0.0000
288 T A 0.0000
289 A A -1.0166
290 A A 0.0000
291 I A 0.0000
292 R A -2.2834
293 H A -1.4851
294 L A 0.0000
295 K A -1.2252
296 T A -0.6853
297 S A -0.4260
298 T A -0.3298
299 W A 0.2189
300 E A 0.0000
301 R A 0.0000
302 E A -2.3461
303 R A -1.7562
304 H A 0.0000
305 Q A -2.5147
306 D A -2.4995
307 R A 0.0000
308 A A 0.0000
309 A A -1.4287
310 R A -1.8518
311 L A 0.0000
312 K A -0.6775
313 A A -0.5899
314 V A -0.8478
315 L A 0.0000
316 N A -1.2081
317 T A -0.7253
318 A A -1.0284
319 G A 0.0000
320 L A 0.0000
321 P A 0.1695
322 V A 0.1541
323 M A -0.0406
324 P A -0.8491
325 T A -1.4227
326 D A -2.1144
327 T A 0.0000
328 H A 0.0000
329 I A 0.0000
330 V A 0.0000
331 P A 0.0000
332 V A 0.0000
333 F A 0.4506
334 V A 0.0000
335 G A -1.5585
336 D A -2.4318
337 A A -2.9453
338 E A -3.5640
339 R A -3.0151
340 C A 0.0000
341 K A -3.0157
342 K A -2.4854
343 A A 0.0000
344 S A 0.0000
345 D A -2.0493
346 L A -1.7037
347 L A 0.0000
348 L A -1.5879
349 E A -2.7875
350 K A -2.6324
351 H A -1.8805
352 G A -1.6166
353 I A 0.0000
354 Y A -0.1627
355 I A 0.0000
356 Q A -0.2452
357 P A -0.9028
358 I A -0.0036
359 N A -1.1378
360 Y A -0.3897
361 P A -0.1844
362 T A -0.2638
363 V A 0.0000
364 A A -1.0180
365 K A -2.1580
366 G A -1.6695
367 K A -1.6744
368 E A 0.0000
369 R A 0.0000
370 L A 0.0000
371 R A 0.0000
372 I A 0.0000
373 T A 0.0000
374 P A 0.0000
375 S A 0.0000
376 P A 0.0000
377 Y A -0.2625
378 H A 0.0000
379 D A -2.3159
380 D A -3.0393
381 D A -3.4715
382 L A -2.3067
383 M A 0.0000
384 D A -3.7999
385 R A -3.3250
386 L A 0.0000
387 A A 0.0000
388 E A -2.7750
389 A A 0.0000
390 L A 0.0000
391 V A -1.0215
392 D A -1.6824
393 V A 0.0000
394 W A 0.0000
395 E A -2.4801
396 T A -1.4774
397 L A -1.7175
398 E A -2.5347
399 L A 0.0000
400 P A -0.5769
401 L A -0.2325
402 G A -0.5734
403 A A -0.7183
404 K A -1.4862
405 P A -0.4565
406 L A 0.7689
407 A A 0.0152
408 A A -0.4071
409 E A -1.5546
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
FR6A -0.4646 -0.0395 View CSV PDB
VD22A -0.7361 -0.0248 View CSV PDB
VE22A -0.5304 -0.0257 View CSV PDB
FE6A -0.0682 -0.0406 View CSV PDB
LR252A -0.3787 -0.0234 View CSV PDB
LK252A -0.3016 -0.0224 View CSV PDB
FK7A 0.1202 -0.0393 View CSV PDB
FR7A 0.2189 -0.0378 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018