Project name: IES_sol

Status: done

Started: 2025-11-18 10:25:36
Settings
Chain sequence(s) A: MTISVPQLDCPLSRPVHPEGERADAYAVEWLRGVGLMADEADAAPVLAVGLGRLAACYVDENASWDTLAFMTILLAWYAEYDDRAIDSTGAIDGLTDAEVAELHRALGEILRDRPAPDPSDPVQRGLADVWRTLNGLASDWDRAAFVDTTLRYFEANRYERVNIRRGIPPTPSAHIGMRRHGGHVYGMYILGAAVNGYRPERRVLDHAAVRELETLAANYTSWANDLHSFAREHRMGQVNNLVWSVHHHEGLTFQQAADRVADLCDKELAAYLELRQTLPELGIPLTGATGRHVRFLEDMMWSMVDWSARSARYDVVPEAA
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                                          (00:07:41)
[INFO]       Auto_mut: Residue number 317 from chain A and a score of 1.551 (valine) selected for  
                       automated muatation                                                         (00:07:46)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 1.280 (valine) selected for    
                       automated muatation                                                         (00:07:46)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.209 (methionine) selected    
                       for automated muatation                                                     (00:07:46)
[INFO]       Auto_mut: Residue number 3 from chain A and a score of 1.196 (isoleucine) selected    
                       for automated muatation                                                     (00:07:46)
[INFO]       Auto_mut: Residue number 316 from chain A and a score of 1.185 (valine) selected for  
                       automated muatation                                                         (00:07:46)
[INFO]       Auto_mut: Residue number 92 from chain A and a score of 0.997 (isoleucine) selected   
                       for automated muatation                                                     (00:07:46)
[INFO]       Auto_mut: Mutating residue number 317 from chain A (valine) into glutamic acid        (00:07:46)
[INFO]       Auto_mut: Mutating residue number 317 from chain A (valine) into aspartic acid        (00:07:46)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into glutamic acid          (00:07:46)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into lysine                 (00:11:48)
[INFO]       Auto_mut: Mutating residue number 317 from chain A (valine) into arginine             (00:12:00)
[INFO]       Auto_mut: Mutating residue number 317 from chain A (valine) into lysine               (00:12:06)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into aspartic acid          (00:16:36)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into glutamic acid      (00:16:46)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into aspartic acid      (00:17:12)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into arginine               (00:20:39)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into lysine             (00:21:00)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (methionine) into arginine           (00:21:20)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (isoleucine) into glutamic acid      (00:24:23)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (isoleucine) into aspartic acid      (00:24:32)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (valine) into glutamic acid        (00:25:01)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (isoleucine) into lysine             (00:27:33)
[INFO]       Auto_mut: Mutating residue number 3 from chain A (isoleucine) into arginine           (00:27:44)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (valine) into lysine               (00:28:07)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (valine) into aspartic acid        (00:31:08)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (isoleucine) into glutamic acid     (00:31:14)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (isoleucine) into aspartic acid     (00:31:15)
[INFO]       Auto_mut: Mutating residue number 316 from chain A (valine) into arginine             (00:34:12)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (isoleucine) into lysine            (00:34:17)
[INFO]       Auto_mut: Mutating residue number 92 from chain A (isoleucine) into arginine          (00:34:18)
[INFO]       Auto_mut: Effect of mutation residue number 317 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1428 kcal/mol, Difference in average score from 
                       the base case: -0.0309                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 317 from chain A (valine) into lysine:    
                       Energy difference: -0.6949 kcal/mol, Difference in average score from the   
                       base case: -0.0221                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 317 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.1992 kcal/mol, Difference in average score from 
                       the base case: -0.0306                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 317 from chain A (valine) into arginine:  
                       Energy difference: -0.8996 kcal/mol, Difference in average score from the   
                       base case: -0.0213                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.9396 kcal/mol, Difference in average score from  
                       the base case: -0.0365                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into lysine:      
                       Energy difference: -1.3044 kcal/mol, Difference in average score from the   
                       base case: -0.0284                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into aspartic     
                       acid: Energy difference: 1.0221 kcal/mol, Difference in average score from  
                       the base case: -0.0394                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into arginine:    
                       Energy difference: -0.2745 kcal/mol, Difference in average score from the   
                       base case: -0.0303                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into glutamic 
                       acid: Energy difference: -0.0908 kcal/mol, Difference in average score from 
                       the base case: -0.0141                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: 0.1831 kcal/mol, Difference in average score from the    
                       base case: -0.0138                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into aspartic 
                       acid: Energy difference: -0.7001 kcal/mol, Difference in average score from 
                       the base case: -0.0139                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: -0.2595 kcal/mol, Difference in average score  
                       from the base case: -0.0215                                                 (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (isoleucine) into glutamic 
                       acid: Energy difference: 1.6538 kcal/mol, Difference in average score from  
                       the base case: -0.0175                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (isoleucine) into lysine:  
                       Energy difference: 1.8351 kcal/mol, Difference in average score from the    
                       base case: -0.0276                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (isoleucine) into aspartic 
                       acid: Energy difference: 2.5995 kcal/mol, Difference in average score from  
                       the base case: -0.0285                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 3 from chain A (isoleucine) into          
                       arginine: Energy difference: 0.1110 kcal/mol, Difference in average score   
                       from the base case: -0.0287                                                 (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.2504 kcal/mol, Difference in average score from 
                       the base case: -0.0374                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (valine) into lysine:    
                       Energy difference: -0.8632 kcal/mol, Difference in average score from the   
                       base case: -0.0337                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.2044 kcal/mol, Difference in average score from 
                       the base case: -0.0377                                                      (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 316 from chain A (valine) into arginine:  
                       Energy difference: -0.9326 kcal/mol, Difference in average score from the   
                       base case: -0.0377                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.0313 kcal/mol, Difference in average    
                       score from the base case: -0.0413                                           (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.1426 kcal/mol, Difference in average score from the   
                       base case: -0.0337                                                          (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -0.2469 kcal/mol, Difference in average   
                       score from the base case: -0.0344                                           (00:37:30)
[INFO]       Auto_mut: Effect of mutation residue number 92 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.3077 kcal/mol, Difference in average score  
                       from the base case: -0.0344                                                 (00:37:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:40)
Show buried residues
Minimal score value
-3.7461
Maximal score value
1.5513
Average score
-0.8077
Total score value
-259.2833
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 1.2086
2 T A 0.9059
3 I A 1.1955
4 S A 0.6128
5 V A 1.2804
6 P A -0.5755
7 Q A -1.2790
8 L A -1.5997
9 D A -2.2740
10 C A -1.2711
11 P A -0.6791
12 L A 0.0000
13 S A -0.3803
14 R A -0.6681
15 P A -0.3909
16 V A 0.1007
17 H A 0.0000
18 P A -1.4507
19 E A -2.1707
20 G A 0.0000
21 E A -2.9628
22 R A -2.8977
23 A A 0.0000
24 D A 0.0000
25 A A -1.0454
26 Y A -1.0267
27 A A 0.0000
28 V A 0.0000
29 E A -2.3012
30 W A 0.0000
31 L A 0.0000
32 R A -2.3429
33 G A -1.6943
34 V A 0.0000
35 G A -1.2232
36 L A -0.5900
37 M A -1.0600
38 A A -1.8882
39 D A -3.3515
40 E A -3.1149
41 A A -2.2379
42 D A -2.2575
43 A A -1.3422
44 A A -0.2089
45 P A -0.2300
46 V A 0.3285
47 L A 0.2536
48 A A 0.2397
49 V A 0.1178
50 G A 0.0000
51 L A 0.0000
52 G A 0.0000
53 R A -1.1883
54 L A -0.1649
55 A A 0.0000
56 A A 0.0000
57 C A 0.0000
58 Y A 0.0000
59 V A 0.0000
60 D A -2.3392
61 E A -2.5564
62 N A -2.3385
63 A A -1.7938
64 S A -1.2114
65 W A -1.1256
66 D A -1.6549
67 T A -0.9440
68 L A 0.0000
69 A A 0.0000
70 F A 0.0000
71 M A 0.0000
72 T A 0.0000
73 I A 0.0000
74 L A 0.0000
75 L A 0.0000
76 A A 0.0000
77 W A 0.0000
78 Y A -0.2984
79 A A -0.5267
80 E A -0.8378
81 Y A 0.0000
82 D A -1.0014
83 D A -1.0722
84 R A -1.2967
85 A A 0.0000
86 I A 0.0000
87 D A 0.0000
88 S A -0.5688
89 T A -0.7541
90 G A -0.6617
91 A A 0.1247
92 I A 0.9974
93 D A -1.0639
94 G A -0.7360
95 L A -0.7206
96 T A -0.8695
97 D A -1.4809
98 A A -1.4194
99 E A -2.3162
100 V A 0.0000
101 A A -2.2570
102 E A -2.9724
103 L A -2.0223
104 H A 0.0000
105 R A -2.8563
106 A A -2.2626
107 L A 0.0000
108 G A 0.0000
109 E A -2.9067
110 I A 0.0000
111 L A 0.0000
112 R A -2.9565
113 D A -3.7461
114 R A -3.5002
115 P A -2.2701
116 A A -1.8536
117 P A -1.7412
118 D A -1.6465
119 P A -1.4302
120 S A -1.1422
121 D A -1.1532
122 P A -0.8161
123 V A -0.6629
124 Q A 0.0000
125 R A -1.7242
126 G A 0.0000
127 L A 0.0000
128 A A -1.7145
129 D A -1.2878
130 V A 0.0000
131 W A 0.0000
132 R A -2.3565
133 T A -1.3781
134 L A 0.0000
135 N A -1.3526
136 G A -0.9202
137 L A -0.7123
138 A A -1.0580
139 S A -1.4039
140 D A -2.2852
141 W A -1.4992
142 D A -1.2107
143 R A -1.3826
144 A A -0.9242
145 A A -0.6764
146 F A 0.0000
147 V A 0.0000
148 D A -1.5069
149 T A 0.0000
150 T A 0.0000
151 L A -1.0016
152 R A -1.3560
153 Y A 0.0000
154 F A 0.0000
155 E A -1.7228
156 A A 0.0000
157 N A 0.0000
158 R A -1.3139
159 Y A -0.3420
160 E A 0.0000
161 R A 0.0000
162 V A -0.4510
163 N A 0.0000
164 I A -1.0522
165 R A -2.3555
166 R A -2.3151
167 G A -1.2017
168 I A 0.1692
169 P A 0.0000
170 P A -0.1188
171 T A -0.3492
172 P A -0.5003
173 S A -0.1926
174 A A -0.0739
175 H A 0.0000
176 I A -0.0127
177 G A -0.2719
178 M A -0.2581
179 R A -0.4056
180 R A -0.6604
181 H A -0.8875
182 G A 0.0000
183 G A -0.7036
184 H A 0.0000
185 V A 0.0000
186 Y A 0.2463
187 G A 0.0000
188 M A 0.2741
189 Y A 0.0000
190 I A 0.0950
191 L A 0.0000
192 G A 0.0000
193 A A -0.9728
194 A A 0.0000
195 V A -0.2345
196 N A -1.1793
197 G A -1.3486
198 Y A -1.7401
199 R A -2.8097
200 P A 0.0000
201 E A -3.0010
202 R A -3.7380
203 R A -3.4291
204 V A -2.2467
205 L A -2.1306
206 D A -3.0507
207 H A -2.1611
208 A A -1.3141
209 A A -1.1024
210 V A 0.0000
211 R A -2.2548
212 E A -2.2894
213 L A 0.0000
214 E A 0.0000
215 T A -0.9639
216 L A -0.4650
217 A A 0.0000
218 A A 0.0000
219 N A -0.1782
220 Y A 0.0000
221 T A 0.0000
222 S A -0.3552
223 W A 0.0000
224 A A 0.0000
225 N A -0.3998
226 D A 0.0000
227 L A 0.0000
228 H A 0.1875
229 S A 0.0000
230 F A 0.0000
231 A A -0.3076
232 R A -0.8696
233 E A 0.0000
234 H A -1.3092
235 R A -1.7785
236 M A -0.9617
237 G A -0.9808
238 Q A 0.0000
239 V A 0.0000
240 N A 0.0000
241 N A 0.0000
242 L A 0.0000
243 V A 0.0000
244 W A -0.0067
245 S A 0.0000
246 V A 0.0000
247 H A -1.4936
248 H A -1.3557
249 H A -1.7812
250 E A -2.3251
251 G A -1.6875
252 L A -1.3550
253 T A -0.9105
254 F A -0.5096
255 Q A -0.9033
256 Q A -1.8888
257 A A 0.0000
258 A A 0.0000
259 D A -2.5158
260 R A -2.5901
261 V A 0.0000
262 A A -2.4380
263 D A -3.3057
264 L A -2.0944
265 C A 0.0000
266 D A -3.4840
267 K A -2.9463
268 E A -1.8001
269 L A 0.0000
270 A A -1.3134
271 A A -1.3009
272 Y A 0.0000
273 L A -0.8293
274 E A -2.0732
275 L A -1.4482
276 R A -1.3736
277 Q A -2.1665
278 T A -1.5585
279 L A 0.0000
280 P A -1.2756
281 E A -1.8662
282 L A -0.3168
283 G A -0.6847
284 I A 0.0000
285 P A -0.4599
286 L A -0.5499
287 T A -0.4942
288 G A -1.1309
289 A A -1.5840
290 T A -1.1305
291 G A -1.2727
292 R A -2.5646
293 H A 0.0000
294 V A 0.0000
295 R A -1.8347
296 F A 0.0000
297 L A 0.0000
298 E A 0.0000
299 D A 0.0000
300 M A 0.0000
301 M A 0.0000
302 W A 0.0000
303 S A 0.0000
304 M A 0.0000
305 V A -0.5746
306 D A -0.6065
307 W A 0.0000
308 S A 0.0000
309 A A -0.9124
310 R A -1.9011
311 S A -1.1270
312 A A -0.4125
313 R A -0.6845
314 Y A -0.4199
315 D A -0.4410
316 V A 1.1854
317 V A 1.5513
318 P A -0.1008
319 E A -1.2731
320 A A -0.8459
321 A A -0.2748
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
VR316A -0.9326 -0.0377 View CSV PDB
VK5A -1.3044 -0.0284 View CSV PDB
VK316A -0.8632 -0.0337 View CSV PDB
VR317A -0.8996 -0.0213 View CSV PDB
IR92A -0.3077 -0.0344 View CSV PDB
VK317A -0.6949 -0.0221 View CSV PDB
ID92A -0.2469 -0.0344 View CSV PDB
VR5A -0.2745 -0.0303 View CSV PDB
MD1A -0.7001 -0.0139 View CSV PDB
MR1A -0.2595 -0.0215 View CSV PDB
IR3A 0.111 -0.0287 View CSV PDB
IK3A 1.8351 -0.0276 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018