Project name: 4AJY_V130D [mutate: VD130V]

Status: done

Started: 2020-09-18 15:00:01
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 VD130V
Energy difference between WT (input) and mutated protein (by FoldX) 4.0546 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                                                       (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:40)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:19)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:20)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:20)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:25)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:26)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:29)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:30)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:30)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:31)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:31)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:33)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:33)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:34)
Show buried residues
Minimal score value
-4.1894
Maximal score value
2.1973
Average score
-0.6855
Total score value
-101.4485
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 -1.5723
61 P V -0.7171
62 V V 0.4577
63 L V -0.7822
64 R V -1.4009
65 S V -0.4938
66 V V -0.5682
67 N V -1.1827
68 S V -1.6281
69 R V -2.2095
70 E V -2.1121
71 P V -1.6837
72 S V 0.0000
73 Q V -1.6213
74 V V 0.0000
75 I V -0.7069
76 F V 0.0000
77 C V -0.8398
78 N V 0.0000
79 R V -2.4811
80 S V 0.0000
81 P V -1.4811
82 R V -1.9085
83 V V -0.5713
84 V V 0.0000
85 L V 0.2758
86 P V 0.0000
87 V V -0.0330
88 W V 0.0000
89 L V 0.0000
90 N V 0.0000
91 F V 0.2414
92 D V -1.3508
93 G V -1.7260
94 E V -2.3314
95 P V -1.4013
96 Q V -1.0534
97 P V -0.5062
98 Y V -0.0352
99 P V -0.0360
100 T V -0.0386
101 L V 0.0000
102 P V -0.9642
103 P V -1.4406
104 G V -1.3695
105 T V -0.9990
106 G V -1.3925
107 R V -2.1813
108 R V -2.5185
109 I V 0.0000
110 H V -1.8108
111 S V -1.1301
112 Y V -0.9088
113 R V -1.3707
114 G V 0.0000
115 H V 0.0000
116 L V 0.0000
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 -0.4792
123 G V -0.4673
124 T V -0.8803
125 H V 0.0000
126 D V 0.0000
127 G V 0.6687
128 L V 1.3646
129 L V 0.0000
130 D V 0.0000 mutated: VD130V
131 N V -1.3477
132 Q V -0.6036
133 T V -0.4456
134 E V 0.0000
135 L V 0.0000
136 F V 0.0000
137 V V 0.0458
138 P V 0.0000
139 S V 0.6303
140 L V 0.7239
141 N V -0.6389
142 V V 0.3264
143 D V -1.6136
144 G V -1.1132
145 Q V 0.0000
146 P V -0.1726
147 I V 0.0000
148 F V 1.5450
149 A V 0.0000
150 N V -1.0832
151 I V 0.0000
152 T V -0.6173
153 L V 0.0000
154 P V 0.5164
155 V V 2.1973
156 Y V 1.3263
157 T V 0.6679
158 L V 0.8518
159 K V -1.1217
160 E V 0.0000
161 R V -0.1864
162 C V 0.5719
163 L V 0.3801
164 Q V 0.2673
165 V V 1.6991
166 V V 1.4166
167 R V 0.0000
168 S V 0.5607
169 L V 1.4231
170 V V -0.4024
171 K V -2.4119
172 P V -2.7809
173 E V -3.3529
174 N V -2.9430
175 Y V 0.0000
176 R V -4.1894
177 R V -2.9854
178 L V -0.4920
179 D V -1.6358
180 I V 0.4404
181 V V 0.8311
182 R V -1.8934
183 S V -1.1805
184 L V -0.7156
185 Y V -1.9147
186 E V -2.9208
187 D V -2.4505
188 L V 0.0000
189 E V -2.6239
190 D V -1.9373
191 H V -1.9914
192 P V 0.0000
193 N V -1.4488
194 V V -1.1049
195 Q V -2.3756
196 K V -2.3944
197 D V 0.0000
198 L V 0.0000
199 E V -3.3107
200 R V -3.4816
201 L V 0.0000
202 T V 0.0000
203 Q V -2.7138
204 E V -3.1353
205 R V -2.3529
206 I V -0.1531
207 A V -0.2561
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View in 3Dmol
Play the video

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, -0.6855 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
model_5 -0.6855 View CSV PDB
model_6 -0.7541 View CSV PDB
model_9 -0.7546 View CSV PDB
model_3 -0.7611 View CSV PDB
model_11 -0.7677 View CSV PDB
model_7 -0.7803 View CSV PDB
model_1 -0.785 View CSV PDB
input -0.7882 View CSV PDB
model_0 -0.7996 View CSV PDB
model_8 -0.8125 View CSV PDB
model_10 -0.8571 View CSV PDB
model_2 -0.8586 View CSV PDB
model_4 -0.9048 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018