Project name: BpCDA

Status: done

Started: 2026-07-29 13:17:50
Settings
Chain sequence(s) A: MIKLIVNADDFGLTEGTNYGIIDGHINGLVNSTTMMMNMPGTEHAVHLAKEYKTLGVGVHLVLTAGKPLLGDVPSLVSSDGLFHKQSVVWEGKVNPEEVEREWTAQIEKFLSYGLKPTHLDSHHHVHGLPILHDVLERLAATYNVPIRRCEEERAVRPFSDLFYSDFYADGVTEDYFVKLKERVQGEQTVEIMVHPAYIDPELVKRSSYVMDRVKELRILTESELPEGIELVKF
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                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:30)
[INFO]       Auto_mut: Residue number 199 from chain A and a score of 1.767 (isoleucine) selected  
                       for automated muatation                                                     (00:03:31)
[INFO]       Auto_mut: Residue number 211 from chain A and a score of 1.222 (methionine) selected  
                       for automated muatation                                                     (00:03:31)
[INFO]       Auto_mut: Residue number 198 from chain A and a score of 1.164 (tyrosine) selected    
                       for automated muatation                                                     (00:03:31)
[INFO]       Auto_mut: Residue number 19 from chain A and a score of 0.887 (tyrosine) selected for 
                       automated muatation                                                         (00:03:31)
[INFO]       Auto_mut: Residue number 26 from chain A and a score of 0.753 (isoleucine) selected   
                       for automated muatation                                                     (00:03:31)
[INFO]       Auto_mut: Residue number 204 from chain A and a score of 0.652 (valine) selected for  
                       automated muatation                                                         (00:03:31)
[INFO]       Auto_mut: Mutating residue number 199 from chain A (isoleucine) into glutamic acid    (00:03:31)
[INFO]       Auto_mut: Mutating residue number 199 from chain A (isoleucine) into aspartic acid    (00:03:31)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (methionine) into glutamic acid    (00:03:31)
[INFO]       Auto_mut: Mutating residue number 199 from chain A (isoleucine) into arginine         (00:05:07)
[INFO]       Auto_mut: Mutating residue number 199 from chain A (isoleucine) into lysine           (00:05:09)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (methionine) into lysine           (00:05:11)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (methionine) into aspartic acid    (00:06:46)
[INFO]       Auto_mut: Mutating residue number 198 from chain A (tyrosine) into glutamic acid      (00:06:53)
[INFO]       Auto_mut: Mutating residue number 198 from chain A (tyrosine) into aspartic acid      (00:07:04)
[INFO]       Auto_mut: Mutating residue number 211 from chain A (methionine) into arginine         (00:08:21)
[INFO]       Auto_mut: Mutating residue number 198 from chain A (tyrosine) into lysine             (00:08:44)
[INFO]       Auto_mut: Mutating residue number 198 from chain A (tyrosine) into arginine           (00:08:51)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (tyrosine) into glutamic acid       (00:10:06)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (tyrosine) into aspartic acid       (00:10:23)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (isoleucine) into glutamic acid     (00:11:00)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (tyrosine) into lysine              (00:11:47)
[INFO]       Auto_mut: Mutating residue number 19 from chain A (tyrosine) into arginine            (00:11:59)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (isoleucine) into lysine            (00:12:33)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (isoleucine) into aspartic acid     (00:13:36)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (valine) into glutamic acid        (00:13:40)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (valine) into aspartic acid        (00:14:21)
[INFO]       Auto_mut: Mutating residue number 26 from chain A (isoleucine) into arginine          (00:15:07)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (valine) into lysine               (00:15:25)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (valine) into arginine             (00:15:54)
[INFO]       Auto_mut: Effect of mutation residue number 199 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 1.6667 kcal/mol, Difference in average    
                       score from the base case: -0.0470                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 199 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.9296 kcal/mol, Difference in average score     
                       from the base case: -0.0612                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 199 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 2.2987 kcal/mol, Difference in average    
                       score from the base case: -0.0451                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 199 from chain A (isoleucine) into        
                       arginine: Energy difference: 1.0837 kcal/mol, Difference in average score   
                       from the base case: -0.0575                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (methionine) into        
                       glutamic acid: Energy difference: 0.1204 kcal/mol, Difference in average    
                       score from the base case: -0.0424                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (methionine) into        
                       lysine: Energy difference: 0.5342 kcal/mol, Difference in average score     
                       from the base case: -0.0522                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (methionine) into        
                       aspartic acid: Energy difference: 0.9595 kcal/mol, Difference in average    
                       score from the base case: -0.0377                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 211 from chain A (methionine) into        
                       arginine: Energy difference: 0.5466 kcal/mol, Difference in average score   
                       from the base case: -0.0566                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 198 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 2.2663 kcal/mol, Difference in average score from  
                       the base case: -0.0322                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 198 from chain A (tyrosine) into lysine:  
                       Energy difference: 1.4411 kcal/mol, Difference in average score from the    
                       base case: -0.0453                                                          (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 198 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 2.0359 kcal/mol, Difference in average score from  
                       the base case: -0.0434                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 198 from chain A (tyrosine) into          
                       arginine: Energy difference: 2.0919 kcal/mol, Difference in average score   
                       from the base case: -0.0308                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 1.1052 kcal/mol, Difference in average score from  
                       the base case: -0.0321                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (tyrosine) into lysine:   
                       Energy difference: 0.5373 kcal/mol, Difference in average score from the    
                       base case: -0.0386                                                          (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 1.8948 kcal/mol, Difference in average score from  
                       the base case: -0.0314                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 19 from chain A (tyrosine) into arginine: 
                       Energy difference: -1.6540 kcal/mol, Difference in average score from the   
                       base case: -0.0423                                                          (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 0.3258 kcal/mol, Difference in average    
                       score from the base case: -0.0514                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.5599 kcal/mol, Difference in average score from the    
                       base case: -0.0533                                                          (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.3859 kcal/mol, Difference in average    
                       score from the base case: -0.0553                                           (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 26 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.6529 kcal/mol, Difference in average score   
                       from the base case: -0.0507                                                 (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.1633 kcal/mol, Difference in average score from 
                       the base case: -0.0650                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (valine) into lysine:    
                       Energy difference: -0.6925 kcal/mol, Difference in average score from the   
                       base case: -0.0616                                                          (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (valine) into aspartic   
                       acid: Energy difference: 0.6687 kcal/mol, Difference in average score from  
                       the base case: -0.0589                                                      (00:17:52)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (valine) into arginine:  
                       Energy difference: -0.4626 kcal/mol, Difference in average score from the   
                       base case: -0.0664                                                          (00:17:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:57)
Show buried residues
Minimal score value
-3.6233
Maximal score value
1.7674
Average score
-0.7595
Total score value
-177.7346
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 -0.8750
2 I A 0.0000
3 K A -1.5027
4 L A 0.0000
5 I A 0.0000
6 V A 0.0000
7 N A 0.0000
8 A A 0.0000
9 D A 0.0000
10 D A 0.0000
11 F A 0.0000
12 G A 0.0000
13 L A 0.0000
14 T A 0.0000
15 E A -1.7859
16 G A 0.0000
17 T A 0.0000
18 N A 0.0000
19 Y A 0.8872
20 G A 0.0000
21 I A 0.0000
22 I A 0.0000
23 D A 0.0604
24 G A 0.0000
25 H A 0.2768
26 I A 0.7528
27 N A -0.9692
28 G A -1.3188
29 L A 0.0000
30 V A 0.0000
31 N A 0.0000
32 S A 0.0000
33 T A 0.0000
34 T A 0.0000
35 M A 0.0000
36 M A 0.0000
37 M A 0.0000
38 N A -0.7353
39 M A 0.0000
40 P A -1.0261
41 G A 0.0000
42 T A 0.0000
43 E A -2.3763
44 H A -1.7757
45 A A 0.0000
46 V A 0.0000
47 H A -2.3685
48 L A -1.8057
49 A A 0.0000
50 K A -3.2127
51 E A -3.1727
52 Y A -1.8317
53 K A -2.5500
54 T A -1.2524
55 L A 0.0000
56 G A 0.0000
57 V A 0.0000
58 G A 0.0000
59 V A 0.0000
60 H A 0.0000
61 L A 0.0000
62 V A 0.0000
63 L A 0.0000
64 T A -0.9480
65 A A -0.8754
66 G A -0.8206
67 K A -1.5812
68 P A -0.6457
69 L A -0.3428
70 L A -0.6504
71 G A -1.1595
72 D A -1.8121
73 V A 0.0000
74 P A -0.7903
75 S A -0.9816
76 L A 0.0000
77 V A -0.7397
78 S A -0.8853
79 S A -0.9722
80 D A -1.8664
81 G A -1.1052
82 L A -0.6972
83 F A 0.0000
84 H A -1.4030
85 K A -1.7598
86 Q A -1.5351
87 S A -1.3105
88 V A -1.3976
89 V A 0.0000
90 W A -0.8832
91 E A -2.1137
92 G A -1.6022
93 K A -2.3416
94 V A 0.0000
95 N A -1.5482
96 P A -1.8412
97 E A -2.5841
98 E A -2.1126
99 V A 0.0000
100 E A -2.1622
101 R A -2.1941
102 E A 0.0000
103 W A 0.0000
104 T A -1.0078
105 A A -0.8384
106 Q A 0.0000
107 I A 0.0000
108 E A -1.4107
109 K A -1.0079
110 F A 0.0000
111 L A -0.7626
112 S A -0.6522
113 Y A -0.6939
114 G A -0.7427
115 L A -1.1082
116 K A -1.5486
117 P A 0.0000
118 T A -0.6848
119 H A 0.0000
120 L A 0.0000
121 D A 0.0000
122 S A 0.0000
123 H A -0.4138
124 H A -0.5820
125 H A -0.6066
126 V A 0.0000
127 H A 0.0000
128 G A -1.3104
129 L A -0.4311
130 P A -0.5927
131 I A 0.0342
132 L A 0.0000
133 H A 0.0000
134 D A -2.1849
135 V A 0.0000
136 L A 0.0000
137 E A -1.8850
138 R A -2.2204
139 L A 0.0000
140 A A 0.0000
141 A A -1.1040
142 T A -0.7876
143 Y A -1.0175
144 N A -1.3922
145 V A 0.0000
146 P A -0.5548
147 I A 0.0000
148 R A 0.0000
149 R A -1.8173
150 C A 0.0000
151 E A -3.3020
152 E A -3.6233
153 E A -3.2345
154 R A -3.1945
155 A A 0.0000
156 V A -0.3112
157 R A -1.4861
158 P A -1.0295
159 F A -0.0709
160 S A 0.0000
161 D A -1.8058
162 L A -0.6732
163 F A 0.0000
164 Y A -0.2229
165 S A -0.3735
166 D A -0.7775
167 F A 0.0000
168 Y A 0.0234
169 A A -0.6430
170 D A -1.7852
171 G A -1.3445
172 V A 0.0000
173 T A -1.9496
174 E A -3.3468
175 D A -2.8266
176 Y A 0.0000
177 F A 0.0000
178 V A -1.5405
179 K A -2.5220
180 L A 0.0000
181 K A -2.4188
182 E A -3.1763
183 R A -2.8809
184 V A 0.0000
185 Q A -2.5569
186 G A -1.9962
187 E A -2.4244
188 Q A -1.8911
189 T A 0.0000
190 V A 0.0000
191 E A 0.0000
192 I A 0.0000
193 M A 0.1265
194 V A 0.0000
195 H A 0.0000
196 P A 0.0000
197 A A 0.0000
198 Y A 1.1642
199 I A 1.7674
200 D A -0.0154
201 P A -0.6292
202 E A -1.4531
203 L A 0.0000
204 V A 0.6516
205 K A -1.7051
206 R A -1.4363
207 S A -0.4042
208 S A -0.1129
209 Y A 0.6062
210 V A 0.0000
211 M A 1.2220
212 D A -0.4273
213 R A 0.0000
214 V A -0.0187
215 K A -1.0979
216 E A 0.0000
217 L A 0.0000
218 R A -2.8682
219 I A 0.0000
220 L A 0.0000
221 T A -2.0806
222 E A -3.2358
223 S A -2.6876
224 E A -2.5992
225 L A -1.1517
226 P A -1.5848
227 E A -2.1014
228 G A -1.3952
229 I A -1.3112
230 E A -1.5613
231 L A -0.6753
232 V A -0.6672
233 K A -0.9293
234 F A -0.1712
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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
YR19A -1.654 -0.0423 View CSV PDB
VK204A -0.6925 -0.0616 View CSV PDB
VR204A -0.4626 -0.0664 View CSV PDB
ME211A 0.1204 -0.0424 View CSV PDB
IE26A 0.3258 -0.0514 View CSV PDB
MR211A 0.5466 -0.0566 View CSV PDB
IK26A 0.5599 -0.0533 View CSV PDB
YK19A 0.5373 -0.0386 View CSV PDB
IK199A 0.9296 -0.0612 View CSV PDB
IR199A 1.0837 -0.0575 View CSV PDB
YK198A 1.4411 -0.0453 View CSV PDB
YD198A 2.0359 -0.0434 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018