Project name: MbPylRs

Status: done

Started: 2026-07-28 11:54:22
Settings
Chain sequence(s) A: MWSHPQFEKGSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGNDREDYLGKLERDITKFFVDRGFLEIKSPILIPAEYVERMGINNDTELSKQIFRVDKNLCLRPMLAPTLYNYLRKLDRILPGPIKIFEVGPCYRKESDGKEHLEEFTMVDFTQMGSGCTRENLEALIKEFLDYLEIDFEIVGDSCMVYGDTLDIMHGDLELSSAVVGPVSLDREWGIDKPWIGAGFGLERLLKVMHGFKNIKRAS
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                                          (00:05:33)
[INFO]       Auto_mut: Residue number 1 from chain A and a score of 1.618 omitted from automated   
                       muatation (excluded by the user).                                           (00:05:35)
[INFO]       Auto_mut: Residue number 138 from chain A and a score of 1.444 (leucine) selected for 
                       automated muatation                                                         (00:05:35)
[INFO]       Auto_mut: Residue number 2 from chain A and a score of 1.379 omitted from automated   
                       muatation (excluded by the user).                                           (00:05:35)
[INFO]       Auto_mut: Residue number 45 from chain A and a score of 1.008 omitted from automated  
                       muatation (excluded by the user).                                           (00:05:35)
[INFO]       Auto_mut: Residue number 137 from chain A and a score of 0.934 (isoleucine) selected  
                       for automated muatation                                                     (00:05:35)
[INFO]       Auto_mut: Residue number 253 from chain A and a score of 0.909 (methionine) selected  
                       for automated muatation                                                     (00:05:35)
[INFO]       Auto_mut: Residue number 186 from chain A and a score of 0.860 (isoleucine) selected  
                       for automated muatation                                                     (00:05:35)
[INFO]       Auto_mut: Residue number 168 from chain A and a score of 0.631 (leucine) selected for 
                       automated muatation                                                         (00:05:35)
[INFO]       Auto_mut: Residue number 187 from chain A and a score of 0.610 (leucine) selected for 
                       automated muatation                                                         (00:05:35)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (leucine) into glutamic acid       (00:05:35)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (leucine) into aspartic acid       (00:05:35)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (isoleucine) into glutamic acid    (00:05:35)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (leucine) into arginine            (00:08:05)
[INFO]       Auto_mut: Mutating residue number 138 from chain A (leucine) into lysine              (00:08:08)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (isoleucine) into lysine           (00:08:08)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (isoleucine) into aspartic acid    (00:10:44)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (methionine) into glutamic acid    (00:10:48)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (methionine) into aspartic acid    (00:10:50)
[INFO]       Auto_mut: Mutating residue number 137 from chain A (isoleucine) into arginine         (00:13:22)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (methionine) into arginine         (00:13:27)
[INFO]       Auto_mut: Mutating residue number 253 from chain A (methionine) into lysine           (00:13:35)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into glutamic acid    (00:16:02)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into aspartic acid    (00:16:08)
[INFO]       Auto_mut: Mutating residue number 168 from chain A (leucine) into glutamic acid       (00:16:42)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into arginine         (00:18:46)
[INFO]       Auto_mut: Mutating residue number 186 from chain A (isoleucine) into lysine           (00:18:46)
[INFO]       Auto_mut: Mutating residue number 168 from chain A (leucine) into lysine              (00:19:16)
[INFO]       Auto_mut: Mutating residue number 168 from chain A (leucine) into aspartic acid       (00:21:28)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (leucine) into glutamic acid       (00:21:53)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (leucine) into aspartic acid       (00:21:58)
[INFO]       Auto_mut: Mutating residue number 168 from chain A (leucine) into arginine            (00:24:01)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (leucine) into lysine              (00:24:25)
[INFO]       Auto_mut: Mutating residue number 187 from chain A (leucine) into arginine            (00:24:30)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.4583 kcal/mol, Difference in average score from  
                       the base case: -0.0161                                                      (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (leucine) into lysine:   
                       Energy difference: 1.4288 kcal/mol, Difference in average score from the    
                       base case: -0.0122                                                          (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.9448 kcal/mol, Difference in average score from  
                       the base case: -0.0208                                                      (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 138 from chain A (leucine) into arginine: 
                       Energy difference: 1.4390 kcal/mol, Difference in average score from the    
                       base case: -0.0234                                                          (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.0578 kcal/mol, Difference in average    
                       score from the base case: -0.0029                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.8357 kcal/mol, Difference in average score     
                       from the base case: -0.0080                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.8962 kcal/mol, Difference in average    
                       score from the base case: -0.0023                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 137 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.3991 kcal/mol, Difference in average score   
                       from the base case: -0.0080                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (methionine) into        
                       glutamic acid: Energy difference: 2.5345 kcal/mol, Difference in average    
                       score from the base case: -0.0186                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (methionine) into        
                       lysine: Energy difference: 1.6301 kcal/mol, Difference in average score     
                       from the base case: -0.0162                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (methionine) into        
                       aspartic acid: Energy difference: 2.6466 kcal/mol, Difference in average    
                       score from the base case: -0.0160                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 253 from chain A (methionine) into        
                       arginine: Energy difference: 0.4697 kcal/mol, Difference in average score   
                       from the base case: -0.0100                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.2512 kcal/mol, Difference in average    
                       score from the base case: -0.0235                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.7464 kcal/mol, Difference in average score     
                       from the base case: -0.0231                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 1.4521 kcal/mol, Difference in average    
                       score from the base case: -0.0301                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 186 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.4154 kcal/mol, Difference in average score   
                       from the base case: -0.0258                                                 (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 168 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.8476 kcal/mol, Difference in average score from  
                       the base case: 0.0022                                                       (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 168 from chain A (leucine) into lysine:   
                       Energy difference: 1.2019 kcal/mol, Difference in average score from the    
                       base case: 0.0025                                                           (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 168 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.8479 kcal/mol, Difference in average score from  
                       the base case: 0.0042                                                       (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 168 from chain A (leucine) into arginine: 
                       Energy difference: -0.2791 kcal/mol, Difference in average score from the   
                       base case: -0.0016                                                          (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (leucine) into glutamic  
                       acid: Energy difference: 1.9784 kcal/mol, Difference in average score from  
                       the base case: -0.0121                                                      (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (leucine) into lysine:   
                       Energy difference: 0.8164 kcal/mol, Difference in average score from the    
                       base case: -0.0035                                                          (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (leucine) into aspartic  
                       acid: Energy difference: 2.7222 kcal/mol, Difference in average score from  
                       the base case: -0.0141                                                      (00:27:12)
[INFO]       Auto_mut: Effect of mutation residue number 187 from chain A (leucine) into arginine: 
                       Energy difference: 0.7452 kcal/mol, Difference in average score from the    
                       base case: -0.0131                                                          (00:27:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:18)
Show buried residues
Minimal score value
-4.0866
Maximal score value
1.618
Average score
-1.2958
Total score value
-404.2933
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 1.6180
2 W A 1.3785
3 S A 0.1518
4 H A -1.2578
5 P A -0.9011
6 Q A -1.0105
7 F A -0.0127
8 E A -1.9338
9 K A -2.4863
10 G A -2.2888
11 S A -1.8378
12 D A -2.4803
13 S A -1.6891
14 E A -1.6911
15 V A -0.0184
16 N A -1.7893
17 Q A -2.5418
18 E A -3.1273
19 A A -2.2040
20 K A -2.6159
21 P A -1.9094
22 E A -2.0127
23 V A -0.6153
24 K A -1.7215
25 P A -1.4577
26 E A -1.7773
27 V A -0.6189
28 K A -2.0570
29 P A -1.8109
30 E A -2.6395
31 T A -2.0361
32 H A -2.6192
33 I A 0.0000
34 N A -1.9257
35 L A 0.0000
36 K A -0.7584
37 V A 0.0000
38 S A -1.4402
39 D A -2.1267
40 G A -1.5496
41 S A -1.0762
42 S A -1.3614
43 E A -1.7202
44 I A 0.0071
45 F A 1.0075
46 F A -0.0974
47 K A -1.9871
48 I A 0.0000
49 K A -2.5695
50 K A -3.0936
51 T A -1.5952
52 T A -1.7649
53 P A -2.6212
54 L A 0.0000
55 R A -3.6873
56 R A -3.2846
57 L A 0.0000
58 M A 0.0000
59 E A -3.5781
60 A A -2.3585
61 F A 0.0000
62 A A 0.0000
63 K A -3.8065
64 R A -3.4234
65 Q A -2.7066
66 G A -2.6171
67 K A -3.4799
68 E A -3.6621
69 M A -2.9916
70 D A -2.6129
71 S A 0.0000
72 L A 0.0000
73 R A -2.2543
74 F A 0.0000
75 L A -1.0777
76 Y A -0.4786
77 D A -1.2571
78 G A -1.5002
79 I A -0.9473
80 R A -1.8493
81 I A 0.0000
82 Q A -2.5339
83 A A -2.9452
84 D A -3.2190
85 Q A -2.6605
86 T A -2.7530
87 P A 0.0000
88 E A -3.8827
89 D A -3.4654
90 L A -2.4240
91 D A -3.3555
92 M A 0.0000
93 E A -3.4665
94 D A -3.1829
95 N A -2.3682
96 D A -1.7317
97 I A -0.8124
98 I A 0.0000
99 E A -1.7669
100 A A 0.0000
101 H A -2.1259
102 R A -2.1503
103 E A -1.5086
104 Q A -1.1760
105 I A 0.5386
106 G A -0.8461
107 G A -1.9214
108 N A -2.6731
109 D A -3.5896
110 R A -4.0694
111 E A -4.0866
112 D A -3.0533
113 Y A -1.2892
114 L A -0.9296
115 G A -1.8005
116 K A -2.7744
117 L A 0.0000
118 E A -2.1651
119 R A -3.1770
120 D A -2.7339
121 I A 0.0000
122 T A -2.3046
123 K A -3.0681
124 F A 0.0000
125 F A 0.0000
126 V A -1.0667
127 D A -2.1283
128 R A -1.4920
129 G A -0.9912
130 F A 0.0000
131 L A -0.3766
132 E A -1.8568
133 I A 0.0000
134 K A -2.0501
135 S A -0.8234
136 P A 0.0395
137 I A 0.9342
138 L A 1.4435
139 I A 0.0000
140 P A -1.1113
141 A A -2.0705
142 E A -3.0426
143 Y A -1.8257
144 V A 0.0000
145 E A -3.7718
146 R A -3.3476
147 M A 0.0000
148 G A -1.8589
149 I A 0.0000
150 N A -3.9373
151 N A -3.6670
152 D A -3.4433
153 T A -2.7385
154 E A -3.0721
155 L A -2.1416
156 S A 0.0000
157 K A -3.3255
158 Q A -2.1453
159 I A 0.0000
160 F A -0.5888
161 R A -1.7059
162 V A -0.0512
163 D A -2.3753
164 K A -3.0086
165 N A -2.7313
166 L A -1.0363
167 C A 0.0000
168 L A 0.6306
169 R A 0.0000
170 P A 0.0000
171 M A 0.0000
172 L A 0.0000
173 A A 0.0433
174 P A 0.0000
175 T A 0.0000
176 L A 0.0000
177 Y A 0.0000
178 N A -0.6219
179 Y A -0.4664
180 L A 0.0000
181 R A -1.9667
182 K A -1.9609
183 L A 0.0000
184 D A -1.4392
185 R A -1.5881
186 I A 0.8602
187 L A 0.6098
188 P A -0.0856
189 G A -0.7091
190 P A -0.7793
191 I A 0.0000
192 K A -0.6233
193 I A 0.0000
194 F A 0.0000
195 E A 0.0000
196 V A 0.0000
197 G A 0.0000
198 P A -0.1546
199 C A 0.0000
200 Y A -0.9522
201 R A -1.7768
202 K A -2.3368
203 E A -2.4437
204 S A -2.0472
205 D A -2.8713
206 G A -2.5375
207 K A -3.1446
208 E A -2.5899
209 H A -2.7754
210 L A 0.0000
211 E A -2.8195
212 E A -2.5277
213 F A -1.2995
214 T A 0.0000
215 M A 0.0406
216 V A 0.0000
217 D A 0.0000
218 F A 0.0000
219 T A 0.0000
220 Q A -0.5469
221 M A 0.0000
222 G A -1.0874
223 S A -0.6266
224 G A -1.0407
225 C A -1.0978
226 T A -1.8476
227 R A -2.9499
228 E A -3.2817
229 N A -2.6801
230 L A 0.0000
231 E A -2.4839
232 A A -2.1342
233 L A -1.8414
234 I A 0.0000
235 K A -2.9874
236 E A -2.5306
237 F A 0.0000
238 L A 0.0000
239 D A -3.1891
240 Y A -1.3901
241 L A 0.0000
242 E A -2.6349
243 I A 0.0000
244 D A -2.9471
245 F A -2.1879
246 E A -2.0727
247 I A -0.8325
248 V A -0.3719
249 G A -1.3363
250 D A -2.4151
251 S A -1.6064
252 C A -0.1710
253 M A 0.9090
254 V A 0.4770
255 Y A 0.0523
256 G A -0.8401
257 D A -2.1899
258 T A 0.0000
259 L A -1.1468
260 D A -1.1220
261 I A 0.0000
262 M A -1.6022
263 H A -1.9809
264 G A -2.1157
265 D A -2.3237
266 L A 0.0000
267 E A -1.7795
268 L A 0.0000
269 S A 0.0000
270 S A -0.4940
271 A A 0.0000
272 V A 0.0000
273 V A -0.5516
274 G A 0.0000
275 P A -0.8317
276 V A -0.6063
277 S A -0.8497
278 L A 0.0000
279 D A 0.0000
280 R A -3.3167
281 E A -3.1750
282 W A 0.0000
283 G A -2.5249
284 I A 0.0000
285 D A -2.8529
286 K A -2.0558
287 P A -1.0141
288 W A 0.0000
289 I A 0.0000
290 G A 0.0000
291 A A 0.0000
292 G A -0.1099
293 F A 0.0000
294 G A -0.2896
295 L A 0.0000
296 E A 0.0000
297 R A -0.6980
298 L A 0.0000
299 L A 0.0000
300 K A -0.9872
301 V A -0.5761
302 M A -0.2966
303 H A -0.4850
304 G A -0.7869
305 F A -1.3800
306 K A -2.4282
307 N A -2.4709
308 I A 0.0000
309 K A -2.7897
310 R A -2.0845
311 A A 0.0000
312 S A -1.2564
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
LR168A -0.2791 -0.0016 View CSV PDB
IR186A 0.4154 -0.0258 View CSV PDB
IE137A 0.0578 -0.0029 View CSV PDB
IK186A 0.7464 -0.0231 View CSV PDB
MR253A 0.4697 -0.01 View CSV PDB
IR137A 0.3991 -0.008 View CSV PDB
LR187A 0.7452 -0.0131 View CSV PDB
LR138A 1.439 -0.0234 View CSV PDB
LE138A 1.4583 -0.0161 View CSV PDB
MK253A 1.6301 -0.0162 View CSV PDB
LE187A 1.9784 -0.0121 View CSV PDB
LK168A 1.2019 0.0025 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018