Project name: DBmut scFv

Status: done

Started: 2021-03-01 04:11:57
Settings
Chain sequence(s) B: QVQLVESGGGVVQPGRSLRLDCKASGITFSNSGMHWVRQAPGKGLEWVAVIWYDGSKRYYADSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCATNDDYWGQGTGVRVSSGGGGSGGGGSGGGGSEIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQSSNWPRTFGQGTKVEIK
input PDB
Selected Chain(s) B
Distance of aggregation 5 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:01:26)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:01:26)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with B chain(s) selected             (00:01:26)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:01:26)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:26)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:07:58)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:07:59)
[INFO]       Auto_mut: Residue number 135 from chain B and a score of 1.773 (valine) selected for  
                       automated muatation                                                         (00:08:06)
[INFO]       Auto_mut: Residue number 238 from chain B and a score of 1.587 (isoleucine) selected  
                       for automated muatation                                                     (00:08:06)
[INFO]       Auto_mut: Residue number 15 from chain B and a score of 1.570 (valine) selected for   
                       automated muatation                                                         (00:08:06)
[INFO]       Auto_mut: Residue number 31 from chain B and a score of 1.285 (isoleucine) selected   
                       for automated muatation                                                     (00:08:06)
[INFO]       Auto_mut: Residue number 9 from chain B and a score of 1.264 (valine) selected for    
                       automated muatation                                                         (00:08:06)
[INFO]       Auto_mut: Residue number 226 from chain B and a score of 1.128 (tryptophan) selected  
                       for automated muatation                                                     (00:08:06)
[INFO]       Auto_mut: Mutating residue number 135 from chain B (valine) into glutamic acid        (00:08:06)
[INFO]       Auto_mut: Mutating residue number 238 from chain B (isoleucine) into glutamic acid    (00:08:06)
[INFO]       Auto_mut: Mutating residue number 135 from chain B (valine) into aspartic acid        (00:08:06)
[INFO]       Auto_mut: Mutating residue number 135 from chain B (valine) into arginine             (00:12:39)
[INFO]       Auto_mut: Mutating residue number 238 from chain B (isoleucine) into lysine           (00:12:39)
[INFO]       Auto_mut: Mutating residue number 135 from chain B (valine) into lysine               (00:12:57)
[INFO]       Auto_mut: Mutating residue number 238 from chain B (isoleucine) into aspartic acid    (00:17:35)
[INFO]       Auto_mut: Mutating residue number 15 from chain B (valine) into glutamic acid         (00:18:11)
[INFO]       Auto_mut: Mutating residue number 15 from chain B (valine) into aspartic acid         (00:18:21)
[INFO]       Auto_mut: Mutating residue number 238 from chain B (isoleucine) into arginine         (00:22:12)
[INFO]       Auto_mut: Mutating residue number 15 from chain B (valine) into arginine              (00:23:05)
[INFO]       Auto_mut: Mutating residue number 15 from chain B (valine) into lysine                (00:23:18)
[INFO]       Auto_mut: Mutating residue number 31 from chain B (isoleucine) into glutamic acid     (00:27:17)
[INFO]       Auto_mut: Mutating residue number 31 from chain B (isoleucine) into aspartic acid     (00:28:25)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (valine) into glutamic acid          (00:28:41)
[INFO]       Auto_mut: Mutating residue number 31 from chain B (isoleucine) into lysine            (00:31:57)
[INFO]       Auto_mut: Mutating residue number 31 from chain B (isoleucine) into arginine          (00:33:15)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (valine) into lysine                 (00:33:41)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (valine) into aspartic acid          (00:36:44)
[INFO]       Auto_mut: Mutating residue number 226 from chain B (tryptophan) into glutamic acid    (00:38:12)
[INFO]       Auto_mut: Mutating residue number 226 from chain B (tryptophan) into aspartic acid    (00:40:11)
[INFO]       Auto_mut: Mutating residue number 9 from chain B (valine) into arginine               (00:42:18)
[INFO]       Auto_mut: Mutating residue number 226 from chain B (tryptophan) into lysine           (00:43:24)
[INFO]       Auto_mut: Mutating residue number 226 from chain B (tryptophan) into arginine         (00:44:59)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain B (valine) into glutamic   
                       acid: Energy difference: 0.0024 kcal/mol, Difference in average score from  
                       the base case: -0.0145                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain B (valine) into lysine:    
                       Energy difference: -0.0521 kcal/mol, Difference in average score from the   
                       base case: -0.0123                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain B (valine) into aspartic   
                       acid: Energy difference: 0.2733 kcal/mol, Difference in average score from  
                       the base case: -0.0138                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 135 from chain B (valine) into arginine:  
                       Energy difference: -0.1200 kcal/mol, Difference in average score from the   
                       base case: -0.0137                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain B (isoleucine) into        
                       glutamic acid: Energy difference: -0.2089 kcal/mol, Difference in average   
                       score from the base case: -0.0214                                           (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain B (isoleucine) into        
                       lysine: Energy difference: -0.3592 kcal/mol, Difference in average score    
                       from the base case: -0.0206                                                 (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain B (isoleucine) into        
                       aspartic acid: Energy difference: 0.9063 kcal/mol, Difference in average    
                       score from the base case: -0.0213                                           (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 238 from chain B (isoleucine) into        
                       arginine: Energy difference: -0.3277 kcal/mol, Difference in average score  
                       from the base case: -0.0214                                                 (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain B (valine) into glutamic    
                       acid: Energy difference: 0.0761 kcal/mol, Difference in average score from  
                       the base case: -0.0211                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain B (valine) into lysine:     
                       Energy difference: -0.4463 kcal/mol, Difference in average score from the   
                       base case: -0.0213                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain B (valine) into aspartic    
                       acid: Energy difference: 0.5013 kcal/mol, Difference in average score from  
                       the base case: -0.0214                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 15 from chain B (valine) into arginine:   
                       Energy difference: -0.2712 kcal/mol, Difference in average score from the   
                       base case: -0.0223                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain B (isoleucine) into         
                       glutamic acid: Energy difference: 0.5991 kcal/mol, Difference in average    
                       score from the base case: -0.0187                                           (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain B (isoleucine) into lysine: 
                       Energy difference: 0.8393 kcal/mol, Difference in average score from the    
                       base case: -0.0174                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain B (isoleucine) into         
                       aspartic acid: Energy difference: 0.4932 kcal/mol, Difference in average    
                       score from the base case: -0.0188                                           (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 31 from chain B (isoleucine) into         
                       arginine: Energy difference: 0.7428 kcal/mol, Difference in average score   
                       from the base case: -0.0194                                                 (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (valine) into glutamic     
                       acid: Energy difference: 0.4629 kcal/mol, Difference in average score from  
                       the base case: -0.0112                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (valine) into lysine:      
                       Energy difference: -0.0468 kcal/mol, Difference in average score from the   
                       base case: -0.0091                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (valine) into aspartic     
                       acid: Energy difference: 0.5097 kcal/mol, Difference in average score from  
                       the base case: -0.0112                                                      (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 9 from chain B (valine) into arginine:    
                       Energy difference: -0.0240 kcal/mol, Difference in average score from the   
                       base case: -0.0066                                                          (00:50:48)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain B (tryptophan) into        
                       glutamic acid: Energy difference: 1.0856 kcal/mol, Difference in average    
                       score from the base case: -0.0170                                           (00:50:49)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain B (tryptophan) into        
                       lysine: Energy difference: 0.9033 kcal/mol, Difference in average score     
                       from the base case: -0.0176                                                 (00:50:49)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain B (tryptophan) into        
                       aspartic acid: Energy difference: 1.3730 kcal/mol, Difference in average    
                       score from the base case: -0.0158                                           (00:50:49)
[INFO]       Auto_mut: Effect of mutation residue number 226 from chain B (tryptophan) into        
                       arginine: Energy difference: 0.9446 kcal/mol, Difference in average score   
                       from the base case: -0.0185                                                 (00:50:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:51:09)
Show buried residues
Minimal score value
-2.0277
Maximal score value
1.7728
Average score
-0.2933
Total score value
-68.9223
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
5 Q B -1.1983
6 V B 0.0000
7 Q B -1.1257
8 L B 0.0000
9 V B 1.2635
10 E B 0.0000
11 S B -0.1390
12 G B -0.3387
13 G B -0.3062
14 G B -0.1027
15 V B 1.5703
16 V B 0.3145
17 Q B -1.1759
18 P B -0.3905
19 G B -0.8305
20 R B -1.9601
21 S B -0.5145
22 L B -0.0916
23 R B -1.9014
24 L B 0.0000
25 D B -0.2178
26 C B 0.0000
27 K B -0.9837
28 A B 0.0000
29 S B -0.2989
30 G B -0.2526
31 I B 1.2850
32 T B 0.1769
33 F B 0.0000
34 S B -0.3651
35 N B -1.2975
36 S B 0.0000
37 G B 0.1211
38 M B 0.0000
39 H B 0.0000
40 W B 0.0000
41 V B 0.0000
42 R B 0.0000
43 Q B -0.1408
44 A B 0.0000
45 P B -0.3390
46 G B -0.6027
47 K B -0.5841
48 G B 0.0000
49 L B 0.0000
50 E B -0.5131
51 W B 0.0000
52 V B 0.0000
53 A B 0.0000
54 V B 0.0000
55 I B 0.0000
56 W B 0.6256
57 Y B 0.7860
58 D B -1.5151
59 G B -0.3898
60 S B -0.4566
61 K B -1.5683
62 R B -1.5393
63 Y B 0.3288
64 Y B 0.2956
65 A B 0.0000
66 D B -1.9864
67 S B -0.4687
68 V B 0.0000
69 K B -1.9635
70 G B -0.8335
71 R B -0.4099
72 F B 0.0000
73 T B -0.1138
74 I B 0.0000
75 S B -0.1087
76 R B -0.2913
77 D B -0.5424
78 N B -0.5923
79 S B -0.5960
80 K B -1.8647
81 N B -1.0472
82 T B 0.0000
83 L B 0.0000
84 F B 0.2761
85 L B 0.0000
86 Q B -1.0690
87 M B 0.0000
88 N B -0.4254
89 S B -0.2124
90 L B 0.0000
91 R B -1.4881
92 A B -0.5029
93 E B -1.2754
94 D B 0.0000
95 T B 0.0000
96 A B 0.0000
97 V B 0.5943
98 Y B 0.0000
99 Y B 0.0000
100 C B 0.0000
101 A B 0.0000
102 T B 0.0000
103 N B -1.1773
104 D B 0.0000
105 D B -0.3735
106 Y B 0.4914
107 W B 0.2258
108 G B 0.0000
109 Q B -1.0760
110 G B -0.2671
111 T B -0.0952
112 G B -0.3043
113 V B 0.0000
114 R B -1.0811
115 V B 0.0000
116 S B -0.0958
117 S B -0.3220
118 G B -0.6434
119 G B -0.6180
120 G B -0.4091
121 G B -0.5062
122 S B -0.3648
123 G B -0.5435
124 G B -0.6349
125 G B -0.6382
126 G B -0.5915
127 S B -0.3836
128 G B -0.5893
129 G B -0.6355
130 G B -0.6349
131 G B -0.5886
132 S B -0.6269
133 E B -1.8308
134 I B 0.0000
135 V B 1.7728
136 L B 0.0000
137 T B -0.0930
138 Q B -0.1664
139 S B -0.2343
140 P B -0.1517
141 A B 0.0282
142 T B -0.1024
143 L B 0.2277
144 S B -0.1862
145 L B -0.0284
146 S B -0.0851
147 P B -0.2804
148 G B -0.7049
149 E B -1.3896
150 R B -2.0269
151 A B 0.0000
152 T B -0.0531
153 L B 0.0000
154 S B -0.0809
155 C B 0.0000
156 R B -2.0277
157 A B 0.0000
158 S B -0.3615
159 Q B -1.2635
160 S B -0.4434
161 V B 0.0000
162 S B -0.1786
163 S B 0.1137
164 Y B 1.1182
165 L B 0.0000
166 A B 0.0000
167 W B 0.0000
168 Y B 0.0000
169 Q B -0.1223
170 Q B 0.0000
171 K B -0.4862
172 P B -0.4169
173 G B -0.7321
174 Q B -1.2818
175 A B -0.2109
176 P B 0.0000
177 R B -0.8310
178 L B 0.0000
179 L B 0.0000
180 I B 0.0000
181 Y B -0.0101
182 D B -1.5960
183 A B 0.0000
184 S B -0.4396
185 N B -1.4586
186 R B -1.0479
187 A B 0.0000
188 T B -0.1568
189 G B -0.4385
190 I B 0.1188
191 P B -0.0644
192 A B -0.0211
193 R B -0.3079
194 F B 0.0000
195 S B -0.0964
196 G B 0.0000
197 S B -0.1812
198 G B -0.2700
199 S B -0.2882
200 G B -0.1680
201 T B -0.3541
202 D B -1.9814
203 F B 0.0000
204 T B -0.0280
205 L B 0.0000
206 T B -0.0203
207 I B 0.0000
208 S B -0.3346
209 S B -0.2638
210 L B 0.0000
211 E B -0.9265
212 P B -0.7369
213 E B -1.8659
214 D B 0.0000
215 F B 0.2087
216 A B 0.0000
217 V B 0.2019
218 Y B 0.0000
219 Y B 0.0000
220 C B 0.0000
221 Q B 0.0000
222 Q B 0.0000
223 S B -0.1809
224 S B -0.1956
225 N B -0.0793
226 W B 1.1279
227 P B 0.1915
228 R B -0.5662
229 T B -0.1072
230 F B 0.0000
231 G B 0.0000
232 Q B -1.2083
233 G B -0.2752
234 T B 0.0000
235 K B -0.8058
236 V B 0.0000
237 E B -0.2740
238 I B 1.5873
239 K B -1.3234
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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
VK15B -0.4463 -0.0213 View CSV PDB
IR238B -0.3277 -0.0214 View CSV PDB
IK238B -0.3592 -0.0206 View CSV PDB
VR15B -0.2712 -0.0223 View CSV PDB
VR135B -0.12 -0.0137 View CSV PDB
VK135B -0.0521 -0.0123 View CSV PDB
VK9B -0.0468 -0.0091 View CSV PDB
VR9B -0.024 -0.0066 View CSV PDB
ID31B 0.4932 -0.0188 View CSV PDB
IE31B 0.5991 -0.0187 View CSV PDB
WR226B 0.9446 -0.0185 View CSV PDB
WK226B 0.9033 -0.0176 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018