Project name: 4AJY_V74G [mutate: VG74V]

Status: done

Started: 2020-09-18 15:04:15
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues VG74V
Energy difference between WT (input) and mutated protein (by FoldX) 4.65382 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
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 V 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]       FoldX:    Building mutant model                                                       (00:01:41)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:43)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:33)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:23:52)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:23:53)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:23:53)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:23:54)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:23:54)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:23:55)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:23:56)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:23:56)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:23:57)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:23:57)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:23:58)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:23:59)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:23:59)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:24:01)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:24:01)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:24:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:02)
Show buried residues
Minimal score value
-4.1808
Maximal score value
1.9666
Average score
-0.7869
Total score value
-116.4552
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
60 R V -1.7899
61 P V -0.8569
62 V V 0.8552
63 L V 0.0000
64 R V -1.0764
65 S V 0.0000
66 V V -0.2685
67 N V -1.0508
68 S V -1.3867
69 R V -2.3845
70 E V -1.7024
71 P V -1.1565
72 S V 0.0000
73 Q V -0.9580
74 G V 0.0000 mutated: VG74V
75 I V -0.6781
76 F V 0.0000
77 C V 0.0000
78 N V 0.0000
79 R V -2.2267
80 S V 0.0000
81 P V -0.6082
82 R V -0.1399
83 V V 0.7862
84 V V 0.0000
85 L V 0.2361
86 P V 0.0000
87 V V 0.0000
88 W V -0.2707
89 L V 0.0000
90 N V -1.2688
91 F V -1.1427
92 D V -2.4886
93 G V -1.9525
94 E V -2.7812
95 P V -1.6176
96 Q V -0.9573
97 P V -0.2171
98 Y V 0.2875
99 P V -0.0119
100 T V 0.1699
101 L V 0.0000
102 P V -0.3017
103 P V -0.7634
104 G V -1.2364
105 T V -0.9910
106 G V -1.4652
107 R V -1.5528
108 R V -2.1429
109 I V -1.2420
110 H V -1.2848
111 S V 0.0000
112 Y V -0.6747
113 R V -0.6309
114 G V -0.0430
115 H V 0.0000
116 L V 0.6709
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V 0.0000
121 D V 0.0000
122 A V -0.0518
123 G V -0.3779
124 T V -0.7001
125 H V -0.8268
126 D V 0.0000
127 G V -0.2436
128 L V 0.0000
129 L V -0.0762
130 V V 0.0000
131 N V -1.0627
132 Q V -1.4149
133 T V -0.8627
134 E V -0.5979
135 L V 0.1849
136 F V 0.0000
137 V V 1.2596
138 P V 0.0000
139 S V 0.5592
140 L V 0.6272
141 N V 0.0245
142 V V 0.5601
143 D V -1.4647
144 G V -1.3279
145 Q V -1.2382
146 P V -0.5686
147 I V 0.6928
148 F V 0.4859
149 A V 0.0000
150 N V -0.9051
151 I V 0.0000
152 T V -0.5853
153 L V 0.5084
154 P V 0.9404
155 V V 1.9666
156 Y V 0.7448
157 T V 0.2289
158 L V 0.6437
159 K V -1.1235
160 E V -1.3513
161 R V -0.7502
162 C V -0.1140
163 L V 0.0000
164 Q V 0.0000
165 V V 0.8672
166 V V 0.8291
167 R V -0.1993
168 S V 0.5131
169 L V 1.3861
170 V V -0.4311
171 K V -2.1651
172 P V -2.5907
173 E V -3.4167
174 N V -3.1105
175 Y V 0.0000
176 R V -3.5327
177 R V -3.2525
178 L V -1.7122
179 D V -1.8946
180 I V -0.1124
181 V V 0.7769
182 R V -1.5909
183 S V -0.9012
184 L V -1.0475
185 Y V 0.0000
186 E V -3.4497
187 D V -2.8854
188 L V 0.0000
189 E V -3.3808
190 D V -3.4846
191 H V -2.9026
192 P V -1.9334
193 N V -2.1483
194 V V -1.8169
195 Q V -3.0216
196 K V -3.2969
197 D V -2.7504
198 L V 0.0000
199 E V -4.1016
200 R V -4.1808
201 L V -2.5110
202 T V -1.9447
203 Q V -2.5858
204 E V -2.9483
205 R V -1.5502
206 I V 0.7955
207 A V -0.2414
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View in 3Dmol
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.7869 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
input -0.7869 View CSV PDB
model_4 -0.8567 View CSV PDB
model_0 -0.8957 View CSV PDB
model_9 -0.9002 View CSV PDB
model_11 -0.9301 View CSV PDB
model_1 -0.9445 View CSV PDB
model_8 -0.9506 View CSV PDB
model_6 -1.001 View CSV PDB
model_3 -1.0042 View CSV PDB
model_10 -1.0392 View CSV PDB
model_2 -1.0406 View CSV PDB
model_7 -1.0443 View CSV PDB
model_5 -1.105 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018