Project name: DMSIRT

Status: done

Started: 2026-06-15 18:36:33
Settings
Chain sequence(s) A: MSCNYADGLSAYDNKGILGAPESFDSDEVVAEKCQELAELIKKSGHVVLHTGAGISTSAGIPDFRGPKGVWTLEEKGEKPDFNVSFDEARPTKTHMAIIALIESGYVQYVISQNIDGLHLKSGLDRKYLSELHGNIYIEQCKKCRRQFVSPSAVETVGQKSLQRACKSSMDSKGRSCRSGILYDNVLDWEHDLPENDLEMGVMHSTVADLNIALGTTLQIVPSGDLPLKNLKCGGKFVICNLQPTKHDKKANLIISSYVDVVLSKVCKLLGVEIPEYSEASDPTKQSKPMEWTIPTSNVNTFHRQYKKYVYFIYYLL
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                                        (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:06:30)
[INFO]       Auto_mut: Residue number 315 from chain A and a score of 3.964 (tyrosine) selected    
                       for automated muatation                                                     (00:06:32)
[INFO]       Auto_mut: Residue number 316 from chain A and a score of 3.907 (leucine) selected for 
                       automated muatation                                                         (00:06:32)
[INFO]       Auto_mut: Residue number 314 from chain A and a score of 3.758 (tyrosine) selected    
                       for automated muatation                                                     (00:06:32)
[INFO]       Auto_mut: Residue number 317 from chain A and a score of 3.247 omitted from automated 
                       muatation (excluded by the user).                                           (00:06:32)
[INFO]       Auto_mut: Residue number 312 from chain A and a score of 3.156 (phenylalanine)        
                       selected for automated muatation                                            (00:06:32)
[INFO]       Auto_mut: Residue number 311 from chain A and a score of 2.201 (tyrosine) selected    
                       for automated muatation                                                     (00:06:32)
[INFO]       Auto_mut: Residue number 258 from chain A and a score of 1.748 (tyrosine) selected    
                       for automated muatation                                                     (00:06:32)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (tyrosine) into glutamic acid      (00:06:32)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (tyrosine) into aspartic acid      (00:06:32)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (leucine) into glutamic acid       (00:06:32)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (leucine) into lysine              (00:09:58)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (tyrosine) into arginine           (00:10:02)
[INFO]       Auto_mut: Mutating residue number 315 from chain A (tyrosine) into lysine             (00:10:03)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (leucine) into aspartic acid       (00:13:37)
[INFO]       Auto_mut: Mutating residue number 314 from chain A (tyrosine) into glutamic acid      (00:13:39)
[INFO]       Auto_mut: Mutating residue number 314 from chain A (tyrosine) into aspartic acid      (00:13:40)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (leucine) into arginine            (00:17:12)
[INFO]       Auto_mut: Mutating residue number 314 from chain A (tyrosine) into lysine             (00:17:33)
[INFO]       Auto_mut: Mutating residue number 314 from chain A (tyrosine) into arginine           (00:17:34)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 312 from chain A (phenylalanine) into glutamic acid (00:20:46)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 312 from chain A (phenylalanine) into aspartic acid (00:21:36)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into glutamic acid      (00:21:52)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (phenylalanine) into lysine        (00:24:20)
[INFO]       Auto_mut: Mutating residue number 312 from chain A (phenylalanine) into arginine      (00:25:07)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into lysine             (00:25:30)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into aspartic acid      (00:28:04)
[INFO]       Auto_mut: Mutating residue number 258 from chain A (tyrosine) into glutamic acid      (00:28:42)
[INFO]       Auto_mut: Mutating residue number 258 from chain A (tyrosine) into aspartic acid      (00:29:22)
[INFO]       Auto_mut: Mutating residue number 311 from chain A (tyrosine) into arginine           (00:31:27)
[INFO]       Auto_mut: Mutating residue number 258 from chain A (tyrosine) into lysine             (00:32:15)
[INFO]       Auto_mut: Mutating residue number 258 from chain A (tyrosine) into arginine           (00:32:44)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.9694 kcal/mol, Difference in average score from  
                       the base case: -0.0194                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.3186 kcal/mol, Difference in average score from the    
                       base case: -0.0177                                                          (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.3100 kcal/mol, Difference in average score from  
                       the base case: -0.0191                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 315 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.3299 kcal/mol, Difference in average score   
                       from the base case: -0.0227                                                 (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.2569 kcal/mol, Difference in average score from  
                       the base case: -0.0175                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (leucine) into lysine:   
                       Energy difference: 0.0280 kcal/mol, Difference in average score from the    
                       base case: -0.0175                                                          (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (leucine) into aspartic  
                       acid: Energy difference: 0.5623 kcal/mol, Difference in average score from  
                       the base case: -0.0136                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (leucine) into arginine: 
                       Energy difference: 0.0463 kcal/mol, Difference in average score from the    
                       base case: -0.0209                                                          (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.3965 kcal/mol, Difference in average score from  
                       the base case: -0.0099                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.6340 kcal/mol, Difference in average score from the    
                       base case: -0.0178                                                          (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.8952 kcal/mol, Difference in average score from  
                       the base case: -0.0152                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 314 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.7781 kcal/mol, Difference in average score   
                       from the base case: -0.0125                                                 (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 1.0148 kcal/mol, Difference in average    
                       score from the base case: -0.0202                                           (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (phenylalanine) into     
                       lysine: Energy difference: 0.4014 kcal/mol, Difference in average score     
                       from the base case: -0.0195                                                 (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 1.4482 kcal/mol, Difference in average    
                       score from the base case: -0.0177                                           (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 312 from chain A (phenylalanine) into     
                       arginine: Energy difference: 0.7742 kcal/mol, Difference in average score   
                       from the base case: -0.0220                                                 (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.6707 kcal/mol, Difference in average score from  
                       the base case: -0.0234                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into lysine:  
                       Energy difference: 0.8780 kcal/mol, Difference in average score from the    
                       base case: -0.0278                                                          (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 1.1714 kcal/mol, Difference in average score from  
                       the base case: -0.0271                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 311 from chain A (tyrosine) into          
                       arginine: Energy difference: 0.4760 kcal/mol, Difference in average score   
                       from the base case: -0.0278                                                 (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 258 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.4957 kcal/mol, Difference in average score from  
                       the base case: -0.0090                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 258 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.0795 kcal/mol, Difference in average score from the   
                       base case: 0.0012                                                           (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 258 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: -0.3797 kcal/mol, Difference in average score from 
                       the base case: -0.0022                                                      (00:36:31)
[INFO]       Auto_mut: Effect of mutation residue number 258 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.2587 kcal/mol, Difference in average score  
                       from the base case: -0.0015                                                 (00:36:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:36:38)
Show buried residues
Minimal score value
-4.5871
Maximal score value
3.9638
Average score
-0.84
Total score value
-266.2723
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 -0.3047
2 S A -0.3706
3 C A 0.0000
4 N A -1.0051
5 Y A -0.8639
6 A A -1.1110
7 D A -2.1308
8 G A -1.5082
9 L A -0.5430
10 S A -0.5748
11 A A -0.5842
12 Y A -0.9730
13 D A -2.2659
14 N A -1.9139
15 K A -1.1300
16 G A -0.2711
17 I A 0.9865
18 L A 0.2816
19 G A -0.5767
20 A A -0.1753
21 P A -0.9465
22 E A -1.0661
23 S A -0.1122
24 F A 1.1741
25 D A -0.0142
26 S A -1.3138
27 D A -2.5331
28 E A -2.9171
29 V A -1.4482
30 V A 0.0000
31 A A -2.4370
32 E A -3.2984
33 K A -2.6298
34 C A 0.0000
35 Q A -3.0641
36 E A -3.6427
37 L A 0.0000
38 A A 0.0000
39 E A -3.4835
40 L A -2.6392
41 I A 0.0000
42 K A -3.3384
43 K A -3.1340
44 S A -2.1783
45 G A -1.4888
46 H A -1.1350
47 V A 0.0000
48 V A 0.0000
49 L A 0.0000
50 H A 0.0000
51 T A 0.0000
52 G A 0.0000
53 A A -0.1640
54 G A -0.0410
55 I A 0.0000
56 S A 0.0000
57 T A -0.1459
58 S A -0.5684
59 A A -1.1865
60 G A -1.1458
61 I A 0.0000
62 P A -0.9189
63 D A -0.6093
64 F A -0.4329
65 R A -0.2220
66 G A 0.0000
67 P A -1.2668
68 K A -2.5754
69 G A 0.0000
70 V A 0.0000
71 W A 0.0000
72 T A 0.0000
73 L A -3.6830
74 E A -4.4002
75 E A -3.9729
76 K A -4.0700
77 G A -3.5914
78 E A -4.5871
79 K A -4.0666
80 P A 0.0000
81 D A -2.7598
82 F A -1.3238
83 N A -1.7040
84 V A -1.3437
85 S A -1.1564
86 F A 0.0000
87 D A -1.9720
88 E A -2.7786
89 A A 0.0000
90 R A -2.7731
91 P A 0.0000
92 T A 0.0000
93 K A -1.7249
94 T A 0.0000
95 H A 0.0000
96 M A 0.0000
97 A A 0.0000
98 I A 0.0000
99 I A -0.5969
100 A A 0.0000
101 L A 0.0000
102 I A 0.0000
103 E A -1.9734
104 S A -1.4380
105 G A -1.3222
106 Y A -1.0961
107 V A 0.0000
108 Q A -0.7495
109 Y A 0.0000
110 V A 0.0000
111 I A 0.0000
112 S A 0.0000
113 Q A -0.1385
114 N A 0.0000
115 I A 0.0000
116 D A 0.0000
117 G A 0.0000
118 L A 0.0000
119 H A 0.0000
120 L A 0.0000
121 K A 0.0000
122 S A 0.0000
123 G A -0.7238
124 L A 0.0000
125 D A -1.5827
126 R A 0.0000
127 K A -2.0367
128 Y A -0.7607
129 L A 0.0000
130 S A 0.0000
131 E A 0.0000
132 L A 0.0000
133 H A -0.3570
134 G A 0.0000
135 N A 0.0000
136 I A 0.0000
137 Y A 0.0000
138 I A 0.0000
139 E A 0.0000
140 Q A -1.2330
141 C A 0.0000
142 K A -2.1567
143 K A -2.7283
144 C A -2.0171
145 R A -2.6834
146 R A -1.9593
147 Q A 0.0000
148 F A 0.0000
149 V A 0.0000
150 S A -0.6627
151 P A -1.2743
152 S A -1.0626
153 A A -0.6851
154 V A 0.0000
155 E A -1.9171
156 T A -1.2070
157 V A 0.0000
158 G A 0.0000
159 Q A -0.8950
160 K A -1.5424
161 S A -1.1316
162 L A 0.0000
163 Q A -1.5847
164 R A -1.3532
165 A A -0.8486
166 C A -1.2955
167 K A -1.0453
168 S A 0.0000
169 S A -0.5674
170 M A -0.7790
171 D A -1.4022
172 S A -1.4681
173 K A -2.4991
174 G A -1.9540
175 R A -2.6924
176 S A -1.6674
177 C A -1.6083
178 R A -2.3087
179 S A -1.2679
180 G A 0.0000
181 I A -0.8097
182 L A 0.0000
183 Y A -0.7021
184 D A 0.0000
185 N A 0.0000
186 V A 0.0000
187 L A -0.7660
188 D A -0.9578
189 W A -1.0920
190 E A -2.3089
191 H A -2.1345
192 D A -2.6114
193 L A -1.6635
194 P A -1.5212
195 E A -2.4899
196 N A -1.7194
197 D A 0.0000
198 L A -1.1044
199 E A -1.7677
200 M A 0.0000
201 G A 0.0000
202 V A -0.1890
203 M A 0.0000
204 H A 0.0000
205 S A 0.0000
206 T A 0.0000
207 V A 0.0000
208 A A 0.0000
209 D A -1.5141
210 L A 0.0000
211 N A 0.0000
212 I A 0.0000
213 A A 0.0000
214 L A 0.0000
215 G A 0.0000
216 T A 0.0000
217 T A -0.3325
218 L A 0.0000
219 Q A 0.0172
220 I A 0.6918
221 V A 1.5568
222 P A 0.7907
223 S A 0.0000
224 G A 0.0000
225 D A -0.7980
226 L A 0.0000
227 P A 0.0000
228 L A -0.9920
229 K A -1.1623
230 N A 0.0000
231 L A -1.4302
232 K A -1.8470
233 C A -0.7229
234 G A -1.2447
235 G A -1.4513
236 K A -1.7929
237 F A 0.0000
238 V A 0.0000
239 I A 0.0000
240 C A 0.0000
241 N A 0.0000
242 L A 0.2162
243 Q A -0.5670
244 P A -0.8245
245 T A -1.3305
246 K A -2.4103
247 H A -2.3264
248 D A -2.3761
249 K A -3.0226
250 K A -2.8203
251 A A -1.8590
252 N A -1.9091
253 L A -1.0207
254 I A -0.1217
255 I A 0.0000
256 S A 0.7118
257 S A 0.0000
258 Y A 1.7477
259 V A 0.0000
260 D A 0.0745
261 V A 0.8006
262 V A 0.0000
263 L A 0.0000
264 S A -0.7660
265 K A -0.8940
266 V A 0.0000
267 C A 0.0000
268 K A -1.9992
269 L A -0.8144
270 L A 0.0000
271 G A -1.1752
272 V A -1.5159
273 E A -2.3304
274 I A -1.5082
275 P A -1.4179
276 E A -2.1438
277 Y A -1.6817
278 S A -1.7717
279 E A -2.6312
280 A A -1.4246
281 S A -1.1948
282 D A 0.0000
283 P A 0.0000
284 T A 0.0000
285 K A -2.9400
286 Q A -2.5941
287 S A -1.8947
288 K A -2.5280
289 P A -1.7184
290 M A -1.3827
291 E A -1.8738
292 W A 0.0000
293 T A -1.1378
294 I A 0.0000
295 P A -0.9916
296 T A -0.8738
297 S A -1.1177
298 N A -1.6263
299 V A 0.0000
300 N A -2.4424
301 T A -1.7794
302 F A -2.0659
303 H A -2.8960
304 R A -3.6390
305 Q A -2.8214
306 Y A -1.8132
307 K A -2.6013
308 K A -2.1142
309 Y A -0.1369
310 V A 0.9966
311 Y A 2.2015
312 F A 3.1558
313 I A 0.0000
314 Y A 3.7576
315 Y A 3.9638
316 L A 3.9073
317 L A 3.2467
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
YD258A -0.3797 -0.0022 View CSV PDB
YR258A -0.2587 -0.0015 View CSV PDB
LK316A 0.028 -0.0175 View CSV PDB
LR316A 0.0463 -0.0209 View CSV PDB
YR315A 0.3299 -0.0227 View CSV PDB
YR311A 0.476 -0.0278 View CSV PDB
YK315A 0.3186 -0.0177 View CSV PDB
FK312A 0.4014 -0.0195 View CSV PDB
YE311A 0.6707 -0.0234 View CSV PDB
FR312A 0.7742 -0.022 View CSV PDB
YK314A 0.634 -0.0178 View CSV PDB
YE314A 0.3965 -0.0099 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018