Project name: 4AJY_I151N [mutate: IN151V]

Status: done

Started: 2020-09-18 15:02:34
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 IN151V
Energy difference between WT (input) and mutated protein (by FoldX) 3.18847 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                                                       (00:01:39)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:42)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:00)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:00)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:01)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:04)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:06)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:06)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:07)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:08)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:08)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:09)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:09)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:12)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:12)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:13)
Show buried residues
Minimal score value
-3.9911
Maximal score value
2.4811
Average score
-0.6931
Total score value
-102.5848
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 -2.3409
61 P V -1.8720
62 V V 0.0000
63 L V -1.3708
64 R V -1.2332
65 S V 0.0279
66 V V 0.9327
67 N V -0.7751
68 S V -1.4682
69 R V -2.3214
70 E V -1.7988
71 P V -1.1741
72 S V 0.0000
73 Q V -1.0095
74 V V 0.0000
75 I V -0.2893
76 F V 0.0000
77 C V -0.6931
78 N V 0.0000
79 R V -2.0588
80 S V -1.0086
81 P V 0.0000
82 R V -2.2513
83 V V -1.1425
84 V V 0.0000
85 L V 0.1643
86 P V 0.0000
87 V V 0.0000
88 W V 0.0031
89 L V 0.0000
90 N V -0.5590
91 F V -0.5261
92 D V -1.9164
93 G V -1.7196
94 E V -2.1809
95 P V -1.2098
96 Q V -1.0322
97 P V -0.4876
98 Y V 0.0002
99 P V -0.1446
100 T V -0.2338
101 L V 0.0000
102 P V -1.2233
103 P V -1.7015
104 G V -1.4093
105 T V -1.0135
106 G V -1.5202
107 R V -1.9529
108 R V -2.1383
109 I V -1.3236
110 H V -1.3942
111 S V 0.0000
112 Y V 0.5194
113 R V -0.4407
114 G V 0.1767
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 -0.4687
123 G V -0.6504
124 T V -0.3366
125 H V 0.6398
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V 0.4465
130 V V 0.0000
131 N V -1.4639
132 Q V -1.9054
133 T V -1.1786
134 E V -0.8768
135 L V 0.0000
136 F V 0.0000
137 V V 0.6106
138 P V 0.0000
139 S V 0.4441
140 L V 1.0155
141 N V -0.2981
142 V V -0.1540
143 D V -2.1313
144 G V -1.1286
145 Q V -0.3490
146 P V -0.2346
147 I V 0.0000
148 F V 1.4058
149 A V 0.0000
150 N V -0.8414
151 N V 0.0000 mutated: IN151V
152 T V 0.1362
153 L V 1.7618
154 P V 1.9388
155 V V 2.4811
156 Y V 1.8070
157 T V 0.7069
158 L V 0.6115
159 K V -1.0911
160 E V -0.5376
161 R V -0.1509
162 C V 0.2472
163 L V 0.0000
164 Q V 0.0000
165 V V 0.9907
166 V V 0.8190
167 R V -0.3736
168 S V 0.4258
169 L V 1.3426
170 V V -0.0995
171 K V -2.0854
172 P V -2.3776
173 E V -2.7936
174 N V -2.4411
175 Y V 0.0000
176 R V -3.9911
177 R V -3.2653
178 L V -1.4793
179 D V -2.4502
180 I V -0.6605
181 V V -0.6686
182 R V -2.2973
183 S V -1.5900
184 L V -1.5146
185 Y V -2.3181
186 E V -2.9759
187 D V -2.3935
188 L V 0.0000
189 E V -2.9680
190 D V -2.9144
191 H V -1.9128
192 P V -1.1468
193 N V 0.0000
194 V V 0.1534
195 Q V -0.8675
196 K V -1.4368
197 D V 0.0000
198 L V 0.0000
199 E V -2.1939
200 R V -2.6539
201 L V -1.8162
202 T V -1.9978
203 Q V -2.6387
204 E V -2.8021
205 R V -1.5888
206 I V 0.7618
207 A V 0.2898
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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, -0.6931 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_11 -0.6931 View CSV PDB
model_8 -0.7216 View CSV PDB
model_3 -0.755 View CSV PDB
model_10 -0.7639 View CSV PDB
input -0.7869 View CSV PDB
model_4 -0.7904 View CSV PDB
model_6 -0.7942 View CSV PDB
model_9 -0.8153 View CSV PDB
model_7 -0.829 View CSV PDB
model_1 -0.8546 View CSV PDB
model_0 -0.8704 View CSV PDB
model_2 -0.8893 View CSV PDB
model_5 -1.0623 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018