Project name: 682c8773a99e0c8

Status: done

Started: 2025-08-13 10:33:43
Settings
Chain sequence(s) A: MFPCLHHSQNLLRAVSNMLQKARQTLEFYPCTSEEIDHEDITKDKTSTVEACLPLELTKNESCLNSRETSFITNGSCLASRKTSFMMALCLSSIYEDLKMYQVEFKTMNAKLLMDPKRQIFLDQNMLAVIDELMQALNFNSETVPQKSSLEEPDFYKTKIKLCILLHAFRIRAVTIDRVMSYLNA
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                                          (00:05:02)
[INFO]       Auto_mut: Residue number 104 from chain A and a score of 1.772 (phenylalanine)        
                       selected for automated muatation                                            (00:05:03)
[INFO]       Auto_mut: Residue number 105 from chain A and a score of 1.182 (isoleucine) selected  
                       for automated muatation                                                     (00:05:03)
[INFO]       Auto_mut: Residue number 204 from chain A and a score of 1.123 (isoleucine) selected  
                       for automated muatation                                                     (00:05:03)
[INFO]       Auto_mut: Residue number 82 from chain A and a score of 0.975 (valine) selected for   
                       automated muatation                                                         (00:05:03)
[INFO]       Auto_mut: Residue number 61 from chain A and a score of 0.905 (phenylalanine)         
                       selected for automated muatation                                            (00:05:03)
[INFO]       Auto_mut: Residue number 34 from chain A and a score of 0.816 (methionine) selected   
                       for automated muatation                                                     (00:05:03)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into glutamic acid    (00:05:03)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 104 from chain A (phenylalanine) into glutamic acid (00:05:03)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 104 from chain A (phenylalanine) into aspartic acid (00:05:03)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (phenylalanine) into arginine      (00:07:32)
[INFO]       Auto_mut: Mutating residue number 104 from chain A (phenylalanine) into lysine        (00:07:37)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into lysine           (00:07:42)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into aspartic acid    (00:10:04)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into glutamic acid    (00:10:24)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into aspartic acid    (00:10:42)
[INFO]       Auto_mut: Mutating residue number 105 from chain A (isoleucine) into arginine         (00:12:23)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into lysine           (00:12:38)
[INFO]       Auto_mut: Mutating residue number 204 from chain A (isoleucine) into arginine         (00:13:01)
[INFO]       Auto_mut: Mutating residue number 82 from chain A (valine) into glutamic acid         (00:14:50)
[INFO]       Auto_mut: Mutating residue number 82 from chain A (valine) into aspartic acid         (00:15:37)
[INFO]       Auto_mut: Mutating residue number 61 from chain A (phenylalanine) into glutamic acid  
                       Mutating residue number 61 from chain A (phenylalanine) into glutamic acid  (00:15:44)
[INFO]       Auto_mut: Mutating residue number 82 from chain A (valine) into lysine                (00:17:42)
[INFO]       Auto_mut: Mutating residue number 82 from chain A (valine) into arginine              (00:17:50)
[INFO]       Auto_mut: Mutating residue number 61 from chain A (phenylalanine) into lysine         (00:18:02)
[INFO]       Auto_mut: Mutating residue number 61 from chain A (phenylalanine) into aspartic acid  
                       Mutating residue number 61 from chain A (phenylalanine) into aspartic acid  (00:20:12)
[INFO]       Auto_mut: Mutating residue number 34 from chain A (methionine) into glutamic acid     (00:20:12)
[INFO]       Auto_mut: Mutating residue number 34 from chain A (methionine) into aspartic acid     (00:20:55)
[INFO]       Auto_mut: Mutating residue number 61 from chain A (phenylalanine) into arginine       (00:22:23)
[INFO]       Auto_mut: Mutating residue number 34 from chain A (methionine) into lysine            (00:22:30)
[INFO]       Auto_mut: Mutating residue number 34 from chain A (methionine) into arginine          (00:23:06)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 0.0310 kcal/mol, Difference in average    
                       score from the base case: -0.0787                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (phenylalanine) into     
                       lysine: Energy difference: -0.2182 kcal/mol, Difference in average score    
                       from the base case: -0.0665                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 0.3539 kcal/mol, Difference in average    
                       score from the base case: -0.0782                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 104 from chain A (phenylalanine) into     
                       arginine: Energy difference: -0.3470 kcal/mol, Difference in average score  
                       from the base case: -0.0786                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: -0.4025 kcal/mol, Difference in average   
                       score from the base case: -0.0646                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       lysine: Energy difference: -0.6232 kcal/mol, Difference in average score    
                       from the base case: -0.0485                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.1301 kcal/mol, Difference in average    
                       score from the base case: -0.0616                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 105 from chain A (isoleucine) into        
                       arginine: Energy difference: -0.1289 kcal/mol, Difference in average score  
                       from the base case: -0.0648                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       glutamic acid: Energy difference: 0.3533 kcal/mol, Difference in average    
                       score from the base case: -0.0673                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       lysine: Energy difference: 0.5306 kcal/mol, Difference in average score     
                       from the base case: -0.0662                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       aspartic acid: Energy difference: 0.7354 kcal/mol, Difference in average    
                       score from the base case: -0.0675                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 204 from chain A (isoleucine) into        
                       arginine: Energy difference: 0.2762 kcal/mol, Difference in average score   
                       from the base case: -0.0614                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 82 from chain A (valine) into glutamic    
                       acid: Energy difference: -0.0364 kcal/mol, Difference in average score from 
                       the base case: -0.0427                                                      (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 82 from chain A (valine) into lysine:     
                       Energy difference: -0.8554 kcal/mol, Difference in average score from the   
                       base case: -0.0528                                                          (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 82 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.0516 kcal/mol, Difference in average score from  
                       the base case: -0.0536                                                      (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 82 from chain A (valine) into arginine:   
                       Energy difference: -0.6187 kcal/mol, Difference in average score from the   
                       base case: -0.0526                                                          (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 61 from chain A (phenylalanine) into      
                       glutamic acid: Energy difference: -0.0402 kcal/mol, Difference in average   
                       score from the base case: -0.0662                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 61 from chain A (phenylalanine) into      
                       lysine: Energy difference: -0.1177 kcal/mol, Difference in average score    
                       from the base case: -0.0551                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 61 from chain A (phenylalanine) into      
                       aspartic acid: Energy difference: -0.3504 kcal/mol, Difference in average   
                       score from the base case: -0.0665                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 61 from chain A (phenylalanine) into      
                       arginine: Energy difference: -0.1496 kcal/mol, Difference in average score  
                       from the base case: -0.0669                                                 (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain A (methionine) into         
                       glutamic acid: Energy difference: 0.4049 kcal/mol, Difference in average    
                       score from the base case: -0.0563                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain A (methionine) into lysine: 
                       Energy difference: 0.5676 kcal/mol, Difference in average score from the    
                       base case: -0.0448                                                          (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain A (methionine) into         
                       aspartic acid: Energy difference: 0.3327 kcal/mol, Difference in average    
                       score from the base case: -0.0584                                           (00:25:29)
[INFO]       Auto_mut: Effect of mutation residue number 34 from chain A (methionine) into         
                       arginine: Energy difference: 0.6685 kcal/mol, Difference in average score   
                       from the base case: -0.0528                                                 (00:25:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:35)
Show buried residues
Minimal score value
-3.4721
Maximal score value
1.7719
Average score
-0.7685
Total score value
-142.1786
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
34 M A 0.8161
35 F A 0.2999
36 P A -0.2641
37 C A 0.0000
38 L A -0.5114
39 H A -0.8233
40 H A -1.1336
41 S A 0.0000
42 Q A -1.5664
43 N A -1.3940
44 L A 0.0000
45 L A -1.0196
46 R A -2.3730
47 A A -1.7732
48 V A 0.0000
49 S A -1.8076
50 N A -2.3373
51 M A 0.0000
52 L A 0.0000
53 Q A -2.5028
54 K A -2.0885
55 A A 0.0000
56 R A -2.2257
57 Q A -2.4151
58 T A -1.5802
59 L A 0.0000
60 E A -1.4020
61 F A 0.9054
62 Y A 0.5685
63 P A -0.5409
64 C A 0.0000
65 T A -1.5940
66 S A -2.0246
67 E A -3.2015
68 E A -3.2135
69 I A -2.6021
70 D A -3.4721
71 H A -3.0605
72 E A -3.1910
73 D A -2.2915
74 I A -1.0922
75 T A 0.0000
76 K A -2.8866
77 D A -2.9361
78 K A -2.2935
79 T A 0.0000
80 S A 0.0000
81 T A 0.0000
82 V A 0.9751
83 E A -0.1265
84 A A 0.0000
85 C A 0.0000
86 L A 0.5375
87 P A 0.1129
88 L A -0.0543
89 E A -1.1266
90 L A 0.3558
91 T A -1.1961
92 K A -2.7858
93 N A -2.7778
94 E A -3.4184
95 S A -2.0532
96 C A -1.4632
97 L A 0.0000
98 N A -2.2304
99 S A -1.9803
100 R A -2.4229
101 E A -1.9000
102 T A -0.4211
103 S A 0.1591
104 F A 1.7719
105 I A 1.1818
106 T A 0.4849
107 N A -0.4744
108 G A 0.0000
109 S A -0.0788
110 C A 0.0000
111 L A -0.6626
112 A A -1.3695
113 S A -1.8338
114 R A -2.7105
115 K A -2.5984
116 T A -1.2693
117 S A -0.5828
118 F A 0.0311
119 M A 0.0000
120 M A 0.0000
121 A A 0.1638
122 L A 0.0000
123 C A 0.0000
124 L A 0.0000
125 S A 0.0000
126 S A 0.0000
127 I A 0.0000
128 Y A 0.0000
129 E A -0.4575
130 D A 0.0000
131 L A 0.0000
132 K A -0.6969
133 M A 0.0556
134 Y A 0.0000
135 Q A 0.0000
136 V A 0.1550
137 E A -0.2005
138 F A 0.0000
139 K A -0.9325
140 T A -0.7226
141 M A 0.0000
142 N A -0.3083
143 A A -0.4272
144 K A -1.0596
145 L A 0.0000
146 L A 0.0894
147 M A -0.8373
148 D A -1.4213
149 P A -1.4344
150 K A -2.7283
151 R A -2.5297
152 Q A -1.4641
153 I A 0.0000
154 F A 0.3213
155 L A 0.0000
156 D A -1.3698
157 Q A -1.8868
158 N A -1.9811
159 M A 0.0000
160 L A 0.0000
161 A A -1.2187
162 V A -1.0364
163 I A 0.0000
164 D A -1.7126
165 E A -1.6599
166 L A 0.0000
167 M A 0.0000
168 Q A -1.2438
169 A A -0.6049
170 L A 0.0000
171 N A 0.0000
172 F A 0.6061
173 N A -1.0932
174 S A -1.4356
175 E A -2.1854
176 T A -1.3708
177 V A -0.8643
178 P A -1.1291
179 Q A -1.6422
180 K A -1.4839
181 S A -0.8431
182 S A -0.6106
183 L A 0.1799
184 E A -2.0417
185 E A -2.8267
186 P A -2.1489
187 D A -2.2578
188 F A -0.9062
189 Y A 0.1002
190 K A -1.5442
191 T A 0.0000
192 K A 0.0000
193 I A -0.0755
194 K A -0.8579
195 L A 0.0000
196 C A 0.0000
197 I A -1.1429
198 L A 0.0000
199 L A 0.0000
200 H A 0.0000
201 A A 0.0000
202 F A 0.0000
203 R A 0.0043
204 I A 1.1232
205 R A 0.6391
206 A A 0.0000
207 V A 0.3449
208 T A 0.3504
209 I A 0.0000
210 D A -0.7504
211 R A -1.0654
212 V A 0.0000
213 M A 0.0000
214 S A -0.5568
215 Y A -0.0389
216 L A -0.0990
217 N A -0.3963
218 A A -0.0562
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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
VK82A -0.8554 -0.0528 View CSV PDB
FR104A -0.347 -0.0786 View CSV PDB
VR82A -0.6187 -0.0526 View CSV PDB
IE105A -0.4025 -0.0646 View CSV PDB
FD61A -0.3504 -0.0665 View CSV PDB
IK105A -0.6232 -0.0485 View CSV PDB
FK104A -0.2182 -0.0665 View CSV PDB
FR61A -0.1496 -0.0669 View CSV PDB
IR204A 0.2762 -0.0614 View CSV PDB
IE204A 0.3533 -0.0673 View CSV PDB
MD34A 0.3327 -0.0584 View CSV PDB
ME34A 0.4049 -0.0563 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018