Project name: normal TDP-43

Status: done

Started: 2025-06-27 05:01:45
Settings
Chain sequence(s) A: MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILHAPDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQGSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNMQREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM
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                                          (00:10:35)
[INFO]       Auto_mut: Residue number 316 from chain A and a score of 2.135 (phenylalanine)        
                       selected for automated muatation                                            (00:10:42)
[INFO]       Auto_mut: Residue number 337 from chain A and a score of 2.087 (methionine) selected  
                       for automated muatation                                                     (00:10:42)
[INFO]       Auto_mut: Residue number 383 from chain A and a score of 2.074 (isoleucine) selected  
                       for automated muatation                                                     (00:10:42)
[INFO]       Auto_mut: Residue number 340 from chain A and a score of 1.944 (leucine) selected for 
                       automated muatation                                                         (00:10:42)
[INFO]       Auto_mut: Residue number 339 from chain A and a score of 1.887 (methionine) selected  
                       for automated muatation                                                     (00:10:42)
[INFO]       Auto_mut: Residue number 336 from chain A and a score of 1.760 (methionine) selected  
                       for automated muatation                                                     (00:10:42)
[INFO]       Auto_mut: Mutating residue number 337 from chain A (methionine) into glutamic acid    (00:10:42)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 316 from chain A (phenylalanine) into glutamic acid (00:10:42)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 316 from chain A (phenylalanine) into aspartic acid (00:10:42)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (phenylalanine) into arginine      (00:15:21)
[INFO]       Auto_mut: Mutating residue number 337 from chain A (methionine) into lysine           (00:15:25)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (phenylalanine) into lysine        (00:15:25)
[INFO]       Auto_mut: Mutating residue number 337 from chain A (methionine) into aspartic acid    (00:19:05)
[INFO]       Auto_mut: Mutating residue number 383 from chain A (isoleucine) into glutamic acid    (00:19:06)
[INFO]       Auto_mut: Mutating residue number 383 from chain A (isoleucine) into aspartic acid    (00:19:11)
[INFO]       Auto_mut: Mutating residue number 383 from chain A (isoleucine) into lysine           (00:22:53)
[INFO]       Auto_mut: Mutating residue number 337 from chain A (methionine) into arginine         (00:22:54)
[INFO]       Auto_mut: Mutating residue number 383 from chain A (isoleucine) into arginine         (00:22:56)
[INFO]       Auto_mut: Mutating residue number 340 from chain A (leucine) into glutamic acid       (00:26:28)
[INFO]       Auto_mut: Mutating residue number 340 from chain A (leucine) into aspartic acid       (00:26:29)
[INFO]       Auto_mut: Mutating residue number 339 from chain A (methionine) into glutamic acid    (00:26:42)
[INFO]       Auto_mut: Mutating residue number 340 from chain A (leucine) into lysine              (00:29:58)
[INFO]       Auto_mut: Mutating residue number 340 from chain A (leucine) into arginine            (00:30:00)
[INFO]       Auto_mut: Mutating residue number 339 from chain A (methionine) into lysine           (00:30:24)
[INFO]       Auto_mut: Mutating residue number 339 from chain A (methionine) into aspartic acid    (00:33:34)
[INFO]       Auto_mut: Mutating residue number 336 from chain A (methionine) into glutamic acid    (00:33:37)
[INFO]       Auto_mut: Mutating residue number 336 from chain A (methionine) into aspartic acid    (00:34:02)
[INFO]       Auto_mut: Mutating residue number 339 from chain A (methionine) into arginine         (00:37:03)
[INFO]       Auto_mut: Mutating residue number 336 from chain A (methionine) into lysine           (00:37:11)
[INFO]       Auto_mut: Mutating residue number 336 from chain A (methionine) into arginine         (00:37:29)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.4551 kcal/mol, Difference in average    
                       score from the base case: -0.0242                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.5937 kcal/mol, Difference in average score     
                       from the base case: -0.0313                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.7468 kcal/mol, Difference in average    
                       score from the base case: -0.0274                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.7651 kcal/mol, Difference in average score   
                       from the base case: -0.0319                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 337 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.0097 kcal/mol, Difference in average    
                       score from the base case: -0.0330                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 337 from chain A (methionine) into        
                       lysine: Energy difference: -0.3110 kcal/mol, Difference in average score    
                       from the base case: -0.0354                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 337 from chain A (methionine) into        
                       aspartic acid: Energy difference: -0.0247 kcal/mol, Difference in average   
                       score from the base case: -0.0327                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 337 from chain A (methionine) into        
                       arginine: Energy difference: -0.3455 kcal/mol, Difference in average score  
                       from the base case: -0.0359                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 383 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.6566 kcal/mol, Difference in average   
                       score from the base case: -0.0306                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 383 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.1120 kcal/mol, Difference in average score    
                       from the base case: -0.0299                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 383 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: -0.5376 kcal/mol, Difference in average   
                       score from the base case: -0.0304                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 383 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.1368 kcal/mol, Difference in average score  
                       from the base case: -0.0308                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 340 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.5638 kcal/mol, Difference in average score from  
                       the base case: -0.0391                                                      (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 340 from chain A (leucine) into lysine:   
                       Energy difference: 0.4432 kcal/mol, Difference in average score from the    
                       base case: -0.0381                                                          (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 340 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.4426 kcal/mol, Difference in average score from  
                       the base case: -0.0388                                                      (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 340 from chain A (leucine) into arginine: 
                       Energy difference: 0.3103 kcal/mol, Difference in average score from the    
                       base case: -0.0393                                                          (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 339 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.1730 kcal/mol, Difference in average    
                       score from the base case: -0.0313                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 339 from chain A (methionine) into        
                       lysine: Energy difference: -0.4370 kcal/mol, Difference in average score    
                       from the base case: -0.0329                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 339 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.0366 kcal/mol, Difference in average    
                       score from the base case: -0.0348                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 339 from chain A (methionine) into        
                       arginine: Energy difference: -0.6295 kcal/mol, Difference in average score  
                       from the base case: -0.0332                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 336 from chain A (methionine) into        
                       glutamic acid: Energy difference: -0.2370 kcal/mol, Difference in average   
                       score from the base case: -0.0332                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 336 from chain A (methionine) into        
                       lysine: Energy difference: -0.5619 kcal/mol, Difference in average score    
                       from the base case: -0.0314                                                 (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 336 from chain A (methionine) into        
                       aspartic acid: Energy difference: -0.1111 kcal/mol, Difference in average   
                       score from the base case: -0.0329                                           (00:41:08)
[INFO]       Auto_mut: Effect of mutation residue number 336 from chain A (methionine) into        
                       arginine: Energy difference: -0.7093 kcal/mol, Difference in average score  
                       from the base case: -0.0320                                                 (00:41:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:41:20)
Show buried residues
Minimal score value
-4.6631
Maximal score value
2.1354
Average score
-1.0402
Total score value
-430.6253
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 -0.2232
2 S A -1.4568
3 E A -1.9358
4 Y A -0.5012
5 I A 0.0000
6 R A -1.5291
7 V A 0.0000
8 T A 0.0000
9 E A -3.6431
10 D A -4.6631
11 E A -4.5232
12 N A -4.2119
13 D A -4.6285
14 E A -3.7445
15 P A -2.4583
16 I A -0.9363
17 E A -1.7616
18 I A 0.0000
19 P A -1.0554
20 S A 0.0000
21 E A -2.7883
22 D A -3.3830
23 D A -3.2420
24 G A -2.2147
25 T A -1.4257
26 V A 0.0000
27 L A 0.3108
28 L A 0.4901
29 S A -0.0657
30 T A -0.0726
31 V A 0.0000
32 T A -0.4122
33 A A -0.5141
34 Q A -1.1395
35 F A 0.0000
36 P A -0.6220
37 G A -0.6390
38 A A 0.0000
39 C A -0.0695
40 G A 0.0000
41 L A 0.0000
42 R A -1.6473
43 Y A 0.0000
44 R A -2.1522
45 N A -1.0814
46 P A -0.1609
47 V A 1.0446
48 S A -0.0825
49 Q A -1.0818
50 C A -0.3619
51 M A -1.0171
52 R A -1.9558
53 G A -1.6976
54 V A -1.2063
55 R A -1.5319
56 L A 0.0406
57 V A 0.2255
58 E A -0.9584
59 G A -0.2558
60 I A 0.4111
61 L A 0.0000
62 H A -0.8223
63 A A -1.1020
64 P A -1.5771
65 D A -1.8790
66 A A -0.9968
67 G A -1.2308
68 W A 0.0000
69 G A -1.1229
70 N A -1.2564
71 L A -0.7527
72 V A -1.1021
73 Y A 0.0000
74 V A 0.0000
75 V A 0.0000
76 N A -1.2748
77 Y A -0.9076
78 P A -1.6453
79 K A -3.2934
80 D A -3.9905
81 N A -4.2003
82 K A -4.3986
83 R A -4.0172
84 K A -3.4099
85 M A -1.7329
86 D A -2.8354
87 E A -3.1054
88 T A -2.2909
89 D A -2.2776
90 A A -1.1758
91 S A -0.5232
92 S A -0.3431
93 A A 0.5159
94 V A 1.1353
95 K A -0.7261
96 V A 0.1039
97 K A -1.5947
98 R A -2.0664
99 A A -0.8285
100 V A -0.2277
101 Q A -1.6390
102 K A -1.8241
103 T A -1.0701
104 S A -1.1486
105 D A -0.4306
106 L A 0.0000
107 I A -0.1441
108 V A 0.0000
109 L A 0.2099
110 G A 0.0056
111 L A 0.0000
112 P A -0.6807
113 W A -0.5741
114 K A -1.5592
115 T A 0.0000
116 T A -2.0684
117 E A -2.4493
118 Q A -2.9461
119 D A -2.9578
120 L A 0.0000
121 K A -2.8654
122 E A -2.8577
123 Y A -1.3949
124 F A 0.0000
125 S A -1.1770
126 T A -0.5251
127 F A -0.3183
128 G A -0.9264
129 E A -1.6713
130 V A -0.5356
131 L A 0.8692
132 M A 0.3117
133 V A -0.7114
134 Q A -1.3399
135 V A 0.0000
136 K A -2.1715
137 K A -2.7797
138 D A -1.8240
139 L A -0.3168
140 K A -1.4830
141 T A -1.3667
142 G A -1.4534
143 H A -2.0796
144 S A -1.9573
145 K A -2.2322
146 G A -1.0462
147 F A -0.2363
148 G A 0.0000
149 F A -0.1104
150 V A 0.0000
151 R A -0.5348
152 F A 0.0000
153 T A -1.0121
154 E A -1.5104
155 Y A -1.1360
156 E A -1.5715
157 T A -1.1512
158 Q A 0.0000
159 V A -0.0949
160 K A -1.3652
161 V A 0.0000
162 M A -0.8223
163 S A -1.1970
164 Q A -1.8921
165 R A -1.9832
166 H A 0.0000
167 M A -0.3980
168 I A 0.0000
169 D A -1.6308
170 G A -1.2001
171 R A -1.2139
172 W A -0.2470
173 C A 0.0000
174 D A -1.0494
175 C A 0.0000
176 K A -1.1106
177 L A -1.1641
178 P A 0.0000
179 N A -2.3884
180 S A -1.9028
181 K A -2.5842
182 Q A -3.1229
183 S A -3.0916
184 Q A -3.2354
185 D A -3.3667
186 E A -3.3027
187 P A -1.9324
188 L A -0.8023
189 R A -2.5064
190 S A -2.3165
191 R A -2.7067
192 K A -2.2644
193 V A 0.0000
194 F A 0.2759
195 V A 0.0000
196 G A 0.0000
197 R A -2.2754
198 C A 0.0000
199 T A -2.1436
200 E A -3.0426
201 D A -2.9560
202 M A 0.0000
203 T A -2.0946
204 E A -2.0948
205 D A -3.3911
206 E A -3.1418
207 L A 0.0000
208 R A -3.6287
209 E A -3.5888
210 F A -1.7813
211 F A 0.0000
212 S A -2.0527
213 Q A -1.8528
214 Y A -0.6554
215 G A -1.1895
216 D A -2.3531
217 V A -1.7343
218 M A -0.7511
219 D A -1.7078
220 V A 0.0000
221 F A 0.8413
222 I A 0.0000
223 P A -0.6976
224 K A -1.8930
225 P A -1.7567
226 F A -1.6572
227 R A -2.4268
228 A A -1.5744
229 F A -0.4301
230 A A 0.0000
231 F A 0.6832
232 V A 0.0000
233 T A -1.1937
234 F A 0.0000
235 A A -1.4686
236 D A -2.4021
237 D A -2.4997
238 Q A -2.4100
239 I A -1.5192
240 A A 0.0000
241 Q A -2.6368
242 S A -1.1758
243 L A 0.0000
244 C A -1.4989
245 G A -1.7795
246 E A -2.2656
247 D A -1.7906
248 L A -0.0588
249 I A 1.2961
250 I A 0.0000
251 K A -1.4745
252 G A -0.3395
253 I A 0.1034
254 S A -0.1734
255 V A 0.0000
256 H A -1.3473
257 I A 0.0000
258 S A -1.2706
259 N A -1.8399
260 A A 0.0000
261 E A -2.6386
262 P A -2.5726
263 K A -3.2254
264 H A -3.2485
265 N A -3.3986
266 S A -2.6652
267 N A -3.0567
268 R A -3.7817
269 Q A -2.9796
270 L A -1.4277
271 E A -3.3238
272 R A -3.2726
273 S A -1.8694
274 G A -1.8110
275 R A -1.9451
276 F A 0.2063
277 G A -0.6252
278 G A -1.1406
279 N A -1.6786
280 P A -1.3523
281 G A -0.7557
282 G A -0.0599
283 F A 1.1174
284 G A -0.5041
285 N A -1.7880
286 Q A -2.2562
287 G A -1.1925
288 G A -0.0971
289 F A 1.0814
290 G A -0.1815
291 N A -1.5679
292 S A -1.9304
293 R A -2.5771
294 G A -1.8736
295 G A -1.3611
296 G A -0.8739
297 A A -0.1479
298 G A 0.0914
299 L A 0.8352
300 G A -0.7144
301 N A -2.0473
302 N A -2.6879
303 Q A -2.3644
304 G A -1.8026
305 S A -1.1475
306 N A -1.0627
307 M A 0.0180
308 G A -0.4395
309 G A -0.6009
310 G A -0.2838
311 M A 0.5093
312 N A -0.1184
313 F A 1.6038
314 G A 0.7423
315 A A 1.1329
316 F A 2.1354
317 S A 0.7965
318 I A 1.0734
319 N A -0.1119
320 P A 0.0236
321 A A 0.4215
322 M A 0.9144
323 M A 0.8375
324 A A 0.1976
325 A A 0.4728
326 A A 0.2320
327 Q A -0.6310
328 A A -0.3852
329 A A 0.0010
330 L A 0.4265
331 Q A -0.7109
332 S A -0.1756
333 S A 0.4651
334 W A 0.9054
335 G A 0.5617
336 M A 1.7596
337 M A 2.0872
338 G A 1.3032
339 M A 1.8869
340 L A 1.9439
341 A A 0.3527
342 S A -0.6918
343 Q A -1.8713
344 Q A -2.5599
345 N A -2.8750
346 Q A -2.5014
347 S A -1.5211
348 G A -1.2600
349 P A -0.9216
350 S A -0.9639
351 G A -1.5617
352 N A -2.4342
353 N A -2.8478
354 Q A -3.0055
355 N A -2.8296
356 Q A -2.5941
357 G A -1.7606
358 N A -1.5236
359 M A -0.6492
360 Q A -2.2614
361 R A -3.1910
362 E A -3.3652
363 P A -2.4879
364 N A -2.3514
365 Q A -1.4525
366 A A 0.0310
367 F A 1.4557
368 G A 0.1410
369 S A -0.5530
370 G A -1.6529
371 N A -2.2899
372 N A -1.8393
373 S A -0.6194
374 Y A 0.6616
375 S A -0.0955
376 G A -0.6915
377 S A -1.1878
378 N A -1.7392
379 S A -1.2132
380 G A -0.8583
381 A A 0.2453
382 A A 0.8772
383 I A 2.0743
384 G A 0.9899
385 W A 1.1106
386 G A -0.0890
387 S A -0.2058
388 A A -0.5292
389 S A -0.8733
390 N A -1.4363
391 A A -0.8929
392 G A -0.9119
393 S A -0.7322
394 G A -0.8896
395 S A -0.4753
396 G A -0.0412
397 F A 0.9471
398 N A -0.7970
399 G A -0.5395
400 G A -0.2331
401 F A 1.2987
402 G A 0.3471
403 S A 0.1016
404 S A -0.2842
405 M A -0.0253
406 D A -1.8172
407 S A -1.7319
408 K A -2.4124
409 S A -1.3358
410 S A -0.6994
411 G A -0.3441
412 W A 0.9185
413 G A 0.5155
414 M A 1.0865
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
MR336A -0.7093 -0.032 View CSV PDB
MR339A -0.6295 -0.0332 View CSV PDB
IE383A -0.6566 -0.0306 View CSV PDB
MK336A -0.5619 -0.0314 View CSV PDB
ID383A -0.5376 -0.0304 View CSV PDB
MK339A -0.437 -0.0329 View CSV PDB
MR337A -0.3455 -0.0359 View CSV PDB
MK337A -0.311 -0.0354 View CSV PDB
LR340A 0.3103 -0.0393 View CSV PDB
LD340A 0.4426 -0.0388 View CSV PDB
FE316A 0.4551 -0.0242 View CSV PDB
FK316A 0.5937 -0.0313 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018