Project name: 4AJY_I109N [mutate: IN109V]

Status: done

Started: 2020-09-18 14:58:02
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 IN109V
Energy difference between WT (input) and mutated protein (by FoldX) 2.7303 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                                        (00:01:45)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:21)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:22)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:22)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:23)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:25)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:26)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:27)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:28)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:28)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:29)
[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
-4.3119
Maximal score value
1.9159
Average score
-0.7219
Total score value
-106.8397
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 -2.0163
61 P V -0.7002
62 V V 0.2182
63 L V 0.0449
64 R V -0.4902
65 S V 0.4671
66 V V 1.0465
67 N V 0.0000
68 S V -1.1744
69 R V -2.4809
70 E V -1.8479
71 P V -1.7287
72 S V 0.0000
73 Q V -1.7613
74 V V 0.0000
75 I V -1.0109
76 F V 0.0000
77 C V -1.0325
78 N V 0.0000
79 R V -2.1832
80 S V 0.0000
81 P V -0.7760
82 R V -0.3438
83 V V 0.4037
84 V V 0.0000
85 L V 0.4297
86 P V 0.4355
87 V V 0.2342
88 W V 0.0000
89 L V -0.0192
90 N V 0.0000
91 F V 0.7820
92 D V -0.9147
93 G V -0.9723
94 E V -1.2475
95 P V -0.9342
96 Q V -0.6029
97 P V 0.0295
98 Y V 0.9449
99 P V 0.4519
100 T V 0.3418
101 L V 0.0000
102 P V -0.8376
103 P V -1.0769
104 G V -1.3537
105 T V -1.4326
106 G V -1.6722
107 R V -2.7511
108 R V -3.0973
109 N V -2.5130 mutated: IN109V
110 H V -1.9942
111 S V 0.0000
112 Y V -1.3403
113 R V -1.2686
114 G V -0.1952
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 -0.1647
121 D V 0.0000
122 A V -0.1921
123 G V -0.3793
124 T V -0.1276
125 H V 0.0000
126 D V -0.3915
127 G V 0.0000
128 L V 0.0000
129 L V -0.0958
130 V V 0.0000
131 N V -0.6794
132 Q V -1.4187
133 T V -0.6226
134 E V -0.3612
135 L V 0.1509
136 F V 0.0000
137 V V 1.0904
138 P V 0.0000
139 S V 0.0989
140 L V 0.0937
141 N V -1.7567
142 V V -1.5930
143 D V -2.6284
144 G V -2.0998
145 Q V -1.6754
146 P V -0.8459
147 I V 0.9319
148 F V 1.0018
149 A V 0.0000
150 N V -0.5659
151 I V 0.0000
152 T V -0.6426
153 L V -0.1591
154 P V -0.0070
155 V V 0.3272
156 Y V -0.3542
157 T V -0.0375
158 L V 0.3894
159 K V -0.7280
160 E V -0.8846
161 R V -0.8490
162 C V 0.5373
163 L V 0.0000
164 Q V 0.0000
165 V V 1.9159
166 V V 1.6363
167 R V -0.1239
168 S V 0.9540
169 L V 1.4852
170 V V -0.4707
171 K V -2.4591
172 P V -3.0748
173 E V -4.0223
174 N V -3.4106
175 Y V 0.0000
176 R V -4.3119
177 R V -3.0471
178 L V -0.8850
179 D V -1.7682
180 I V 0.4474
181 V V 0.5371
182 R V -1.9631
183 S V -1.2685
184 L V -0.9271
185 Y V -2.3159
186 E V -3.2026
187 D V -2.4964
188 L V 0.0000
189 E V -3.8831
190 D V -3.0523
191 H V -2.1506
192 P V -1.5618
193 N V -1.4280
194 V V -1.0593
195 Q V -1.5021
196 K V -1.9409
197 D V 0.0000
198 L V 0.0000
199 E V -2.1712
200 R V -2.6418
201 L V 0.0000
202 T V 0.0000
203 Q V -2.4891
204 E V -2.7235
205 R V -1.6925
206 I V 0.5223
207 A V 0.2839
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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, -0.7219 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_10 -0.7219 View CSV PDB
model_7 -0.7391 View CSV PDB
input -0.8074 View CSV PDB
model_2 -0.8079 View CSV PDB
model_9 -0.819 View CSV PDB
model_3 -0.8548 View CSV PDB
model_11 -0.8631 View CSV PDB
model_8 -0.8644 View CSV PDB
model_0 -0.8792 View CSV PDB
model_4 -0.9026 View CSV PDB
model_1 -0.9384 View CSV PDB
model_5 -0.9818 View CSV PDB
model_6 -1.0213 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018