Project name: genF

Status: done

Started: 2026-03-23 11:38:03
Settings
Chain sequence(s) A: LTAAPAGARIAFRTSGTTGEPVAWLRTEAQVRAEAELVLERLLGPVGHVISYAPTTHLYGYLYADVLPRLTGARVEHAWRDPIAPPRIPDGHRTLLVCLPSTWEPLVRHTAELARHSGLIALHSTGPTTPAAHRTAARLRGTGFRAVELLGSTETGAVAHRSLTPEGDPPDPWRLLPDVAWPGADRAGEQRLRVSGPRLARRWDQAAPPADHELPDLVIRAGERSFHHLGRTARLVKVNGRRCDLGRVEALARTCGHGLDAACAAVPDPLRGEHYELYYTAPDPALDPAALRARLARLGPDLPAPRAVHRVARIPRGVTGKVLTSRLRAAAARPRPSQETDHG
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                                          (00:04:01)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.104 (leucine) selected for   
                       automated muatation                                                         (00:04:03)
[INFO]       Auto_mut: Residue number 318 from chain A and a score of 1.091 (valine) selected for  
                       automated muatation                                                         (00:04:03)
[INFO]       Auto_mut: Residue number 83 from chain A and a score of 1.059 (isoleucine) selected   
                       for automated muatation                                                     (00:04:03)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 0.458 (threonine) selected for 
                       automated muatation                                                         (00:04:03)
[INFO]       Auto_mut: Residue number 270 from chain A and a score of 0.436 (leucine) selected for 
                       automated muatation                                                         (00:04:03)
[INFO]       Auto_mut: Residue number 229 from chain A and a score of 0.151 (leucine) selected for 
                       automated muatation                                                         (00:04:03)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into glutamic acid         (00:04:03)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into aspartic acid         (00:04:03)
[INFO]       Auto_mut: Mutating residue number 318 from chain A (valine) into glutamic acid        (00:04:03)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into arginine              (00:05:41)
[INFO]       Auto_mut: Mutating residue number 1 from chain A (leucine) into lysine                (00:05:42)
[INFO]       Auto_mut: Mutating residue number 318 from chain A (valine) into lysine               (00:05:45)
[INFO]       Auto_mut: Mutating residue number 318 from chain A (valine) into aspartic acid        (00:07:30)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (isoleucine) into glutamic acid     (00:07:32)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (isoleucine) into aspartic acid     (00:07:35)
[INFO]       Auto_mut: Mutating residue number 318 from chain A (valine) into arginine             (00:09:10)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (isoleucine) into lysine            (00:09:12)
[INFO]       Auto_mut: Mutating residue number 83 from chain A (isoleucine) into arginine          (00:09:12)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (threonine) into glutamic acid       (00:10:54)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (threonine) into aspartic acid       (00:11:02)
[INFO]       Auto_mut: Mutating residue number 270 from chain A (leucine) into glutamic acid       (00:11:05)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (threonine) into lysine              (00:12:34)
[INFO]       Auto_mut: Mutating residue number 2 from chain A (threonine) into arginine            (00:12:40)
[INFO]       Auto_mut: Mutating residue number 270 from chain A (leucine) into lysine              (00:12:49)
[INFO]       Auto_mut: Mutating residue number 270 from chain A (leucine) into aspartic acid       (00:14:21)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into glutamic acid       (00:14:31)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into aspartic acid       (00:15:21)
[INFO]       Auto_mut: Mutating residue number 270 from chain A (leucine) into arginine            (00:16:07)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into lysine              (00:16:13)
[INFO]       Auto_mut: Mutating residue number 229 from chain A (leucine) into arginine            (00:17:05)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into glutamic    
                       acid: Energy difference: -0.2196 kcal/mol, Difference in average score from 
                       the base case: -0.0116                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into lysine:     
                       Energy difference: -0.0731 kcal/mol, Difference in average score from the   
                       base case: -0.0160                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into aspartic    
                       acid: Energy difference: -0.0877 kcal/mol, Difference in average score from 
                       the base case: -0.0162                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 1 from chain A (leucine) into arginine:   
                       Energy difference: 0.0233 kcal/mol, Difference in average score from the    
                       base case: -0.0301                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 318 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.3491 kcal/mol, Difference in average score from 
                       the base case: -0.0216                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 318 from chain A (valine) into lysine:    
                       Energy difference: -0.0887 kcal/mol, Difference in average score from the   
                       base case: -0.0206                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 318 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.2621 kcal/mol, Difference in average score from 
                       the base case: -0.0212                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 318 from chain A (valine) into arginine:  
                       Energy difference: -0.0841 kcal/mol, Difference in average score from the   
                       base case: -0.0155                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: -0.0762 kcal/mol, Difference in average   
                       score from the base case: -0.0250                                           (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (isoleucine) into lysine: 
                       Energy difference: -0.3107 kcal/mol, Difference in average score from the   
                       base case: -0.0290                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: -0.0901 kcal/mol, Difference in average   
                       score from the base case: -0.0246                                           (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 83 from chain A (isoleucine) into         
                       arginine: Energy difference: -0.2781 kcal/mol, Difference in average score  
                       from the base case: -0.0217                                                 (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (threonine) into glutamic  
                       acid: Energy difference: -0.6669 kcal/mol, Difference in average score from 
                       the base case: -0.0052                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (threonine) into lysine:   
                       Energy difference: -0.4315 kcal/mol, Difference in average score from the   
                       base case: -0.0068                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (threonine) into aspartic  
                       acid: Energy difference: -0.6671 kcal/mol, Difference in average score from 
                       the base case: -0.0046                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 2 from chain A (threonine) into arginine: 
                       Energy difference: -0.9068 kcal/mol, Difference in average score from the   
                       base case: -0.0227                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 270 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.6711 kcal/mol, Difference in average score from  
                       the base case: -0.0189                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 270 from chain A (leucine) into lysine:   
                       Energy difference: 0.0102 kcal/mol, Difference in average score from the    
                       base case: -0.0165                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 270 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.3324 kcal/mol, Difference in average score from  
                       the base case: -0.0114                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 270 from chain A (leucine) into arginine: 
                       Energy difference: 0.3893 kcal/mol, Difference in average score from the    
                       base case: -0.0250                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into glutamic  
                       acid: Energy difference: 2.1857 kcal/mol, Difference in average score from  
                       the base case: -0.0198                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into lysine:   
                       Energy difference: 1.3427 kcal/mol, Difference in average score from the    
                       base case: -0.0176                                                          (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.5282 kcal/mol, Difference in average score from  
                       the base case: -0.0210                                                      (00:18:51)
[INFO]       Auto_mut: Effect of mutation residue number 229 from chain A (leucine) into arginine: 
                       Energy difference: 1.5208 kcal/mol, Difference in average score from the    
                       base case: -0.0154                                                          (00:18:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:58)
Show buried residues
Minimal score value
-3.2242
Maximal score value
1.1044
Average score
-0.9347
Total score value
-320.5975
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 L A 1.1044
2 T A 0.4581
3 A A 0.0602
4 A A -0.3583
5 P A -0.4471
6 A A -0.5695
7 G A -1.1430
8 A A 0.0000
9 R A -2.0904
10 I A 0.0000
11 A A -0.5321
12 F A 0.0000
13 R A -1.8496
14 T A 0.0000
15 S A -1.2099
16 G A -1.5995
17 T A -1.5722
18 T A 0.0000
19 G A -1.7975
20 E A -2.0472
21 P A -1.3354
22 V A -0.7982
23 A A -0.9795
24 W A 0.0000
25 L A 0.0000
26 R A 0.0000
27 T A -1.6456
28 E A -2.3892
29 A A -1.3420
30 Q A -1.3459
31 V A 0.0000
32 R A -2.7358
33 A A -1.6623
34 E A 0.0000
35 A A 0.0000
36 E A -2.7884
37 L A -2.0298
38 V A 0.0000
39 L A -1.7409
40 E A -2.9829
41 R A -2.5703
42 L A -1.3215
43 L A 0.0000
44 G A -1.4349
45 P A -0.9840
46 V A 0.0000
47 G A -1.4705
48 H A 0.0000
49 V A 0.0000
50 I A 0.0000
51 S A 0.0000
52 Y A 0.0000
53 A A 0.0000
54 P A -0.3071
55 T A -0.1227
56 T A -0.2596
57 H A -0.7849
58 L A 0.0000
59 Y A 0.0714
60 G A 0.0000
61 Y A 0.0537
62 L A 0.0000
63 Y A 0.0000
64 A A 0.0000
65 D A -0.6648
66 V A 0.0000
67 L A 0.0000
68 P A 0.0000
69 R A -2.1420
70 L A -1.0097
71 T A -1.0118
72 G A -1.3352
73 A A -1.7688
74 R A -2.3276
75 V A -1.2763
76 E A -1.4922
77 H A -1.1434
78 A A -1.2542
79 W A -0.9459
80 R A -2.4429
81 D A -2.0672
82 P A -0.5386
83 I A 1.0591
84 A A -0.0944
85 P A -0.8461
86 P A -1.2228
87 R A -2.3152
88 I A -2.0668
89 P A -1.8380
90 D A -2.9239
91 G A -2.0923
92 H A -2.4898
93 R A -2.2253
94 T A 0.0000
95 L A 0.0000
96 L A 0.0000
97 V A 0.0000
98 C A 0.0000
99 L A 0.0052
100 P A -0.2168
101 S A -0.2193
102 T A 0.0000
103 W A 0.0000
104 E A -0.9777
105 P A -0.6154
106 L A 0.0000
107 V A 0.0000
108 R A -2.4562
109 H A -1.7657
110 T A 0.0000
111 A A -1.8596
112 E A -2.8328
113 L A 0.0000
114 A A -2.1510
115 R A -2.7826
116 H A -2.3061
117 S A -1.5848
118 G A -1.7292
119 L A 0.0000
120 I A 0.0000
121 A A 0.0000
122 L A 0.0000
123 H A 0.0000
124 S A 0.0000
125 T A -0.1108
126 G A -0.4093
127 P A -0.2983
128 T A -0.1077
129 T A 0.0000
130 P A -0.9027
131 A A -1.0616
132 A A 0.0000
133 H A -1.8596
134 R A -2.6337
135 T A 0.0000
136 A A 0.0000
137 A A -2.6537
138 R A -2.9031
139 L A 0.0000
140 R A -3.0468
141 G A -1.9023
142 T A -1.8328
143 G A -1.6167
144 F A -1.6471
145 R A -2.1123
146 A A 0.0000
147 V A 0.0000
148 E A 0.0000
149 L A 0.0000
150 L A 0.0000
151 G A -0.0655
152 S A -0.0495
153 T A -0.3787
154 E A 0.0000
155 T A 0.0000
156 G A 0.0000
157 A A 0.0000
158 V A 0.0000
159 A A 0.0000
160 H A 0.0000
161 R A -1.1699
162 S A -1.1089
163 L A 0.0000
164 T A 0.0000
165 P A -2.3778
166 E A -2.8590
167 G A -2.2507
168 D A -2.8847
169 P A -2.0296
170 P A -2.0685
171 D A -2.6216
172 P A -1.8277
173 W A 0.0000
174 R A -2.3542
175 L A 0.0000
176 L A 0.0000
177 P A -0.8367
178 D A -0.6047
179 V A 0.0000
180 A A -0.4802
181 W A -0.9923
182 P A -0.8440
183 G A -1.2901
184 A A -1.5362
185 D A -3.1232
186 R A -3.1268
187 A A -1.8226
188 G A -1.8340
189 E A -2.2622
190 Q A -1.7952
191 R A -1.5839
192 L A 0.0000
193 R A -1.5680
194 V A 0.0000
195 S A -0.7373
196 G A -0.5429
197 P A -0.5133
198 R A 0.0000
199 L A 0.0000
200 A A 0.0000
201 R A -0.9797
202 R A -1.4831
203 W A -0.7195
204 D A -1.8285
205 Q A -1.4057
206 A A -0.6229
207 A A -0.4661
208 P A -0.5516
209 P A -0.5832
210 A A -0.3532
211 D A -0.9864
212 H A -0.9977
213 E A -1.3544
214 L A 0.0000
215 P A -0.7690
216 D A 0.0000
217 L A -0.6590
218 V A 0.0000
219 I A -0.6350
220 R A -1.6829
221 A A -0.9611
222 G A -1.8746
223 E A -2.8029
224 R A -2.2638
225 S A -2.0479
226 F A 0.0000
227 H A -1.0631
228 H A -0.4604
229 L A 0.1510
230 G A -0.2425
231 R A -0.6900
232 T A -0.5254
233 A A -0.6139
234 R A -1.2706
235 L A -0.9361
236 V A 0.0000
237 K A -1.2264
238 V A 0.0000
239 N A -1.7557
240 G A -1.5908
241 R A -1.4148
242 R A -1.0773
243 C A 0.0000
244 D A -1.5954
245 L A 0.0000
246 G A -1.4603
247 R A -2.3265
248 V A 0.0000
249 E A -1.3916
250 A A -1.3796
251 L A -0.8047
252 A A 0.0000
253 R A -2.3372
254 T A -1.1705
255 C A 0.0000
256 G A -1.5502
257 H A -1.8608
258 G A -1.6248
259 L A 0.0000
260 D A -1.5202
261 A A 0.0000
262 A A 0.0000
263 C A 0.0000
264 A A 0.0000
265 A A -0.3202
266 V A 0.0000
267 P A -0.2756
268 D A 0.0000
269 P A -0.0323
270 L A 0.4365
271 R A -0.4836
272 G A 0.0000
273 E A 0.0000
274 H A 0.0000
275 Y A 0.0000
276 E A -0.5816
277 L A 0.0000
278 Y A 0.0000
279 Y A 0.0000
280 T A -1.5887
281 A A 0.0000
282 P A -1.2290
283 D A -1.8095
284 P A -1.2857
285 A A -0.8689
286 L A 0.0000
287 D A -1.8764
288 P A -1.2642
289 A A -0.7001
290 A A -0.8055
291 L A 0.0000
292 R A -1.1877
293 A A -0.9872
294 R A -1.4338
295 L A 0.0000
296 A A -1.2508
297 R A -1.9048
298 L A -0.2388
299 G A 0.0000
300 P A -1.3660
301 D A -1.9053
302 L A -1.1930
303 P A -0.8927
304 A A -0.4788
305 P A 0.0000
306 R A -0.9603
307 A A -0.5357
308 V A -0.7683
309 H A -1.1139
310 R A -1.9879
311 V A 0.0000
312 A A -1.1908
313 R A -2.1891
314 I A 0.0000
315 P A -1.7203
316 R A -1.5579
317 G A -0.2392
318 V A 1.0912
319 T A -0.0332
320 G A -0.8136
321 K A -1.6774
322 V A -1.1036
323 L A -1.1765
324 T A -1.1085
325 S A -1.2945
326 R A -2.2234
327 L A 0.0000
328 R A -1.7720
329 A A -1.5363
330 A A -1.8187
331 A A -1.6144
332 A A -1.5226
333 R A -2.5476
334 P A -2.1000
335 R A -2.8044
336 P A -2.2199
337 S A -2.0229
338 Q A -2.8159
339 E A -3.2242
340 T A -2.5626
341 D A -3.1669
342 H A -2.3695
343 G A -1.5006
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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
TR2A -0.9068 -0.0227 View CSV PDB
IK83A -0.3107 -0.029 View CSV PDB
VE318A -0.3491 -0.0216 View CSV PDB
IR83A -0.2781 -0.0217 View CSV PDB
VD318A -0.2621 -0.0212 View CSV PDB
LD1A -0.0877 -0.0162 View CSV PDB
LK1A -0.0731 -0.016 View CSV PDB
TK2A -0.4315 -0.0068 View CSV PDB
LK270A 0.0102 -0.0165 View CSV PDB
LR270A 0.3893 -0.025 View CSV PDB
LK229A 1.3427 -0.0176 View CSV PDB
LR229A 1.5208 -0.0154 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018