Project name: 4AJY_L188P [mutate: LP188V]

Status: done

Started: 2020-09-18 14:54:47
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 LP188V
Energy difference between WT (input) and mutated protein (by FoldX) 7.23227 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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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)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with V chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:50)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:55)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:47)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:26:41)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:26:42)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:26:42)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:26:43)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:26:44)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:26:44)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:26:45)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:26:46)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:26:46)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:26:47)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:26:47)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:26:48)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:26:49)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:26:50)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:26:51)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:26:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:52)
Show buried residues

Minimal score value
-4.1808
Maximal score value
1.9666
Average score
-0.7826
Total score value
-115.8181

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 -0.2682
67 N V -1.0505
68 S V -1.3862
69 R V -2.3840
70 E V -1.7018
71 P V -1.1561
72 S V 0.0000
73 Q V -0.9603
74 V V 0.0000
75 I V -0.6808
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 -0.1400
83 V V 0.7861
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 -1.4659
107 R V -1.5540
108 R V -2.1453
109 I V -1.2456
110 H V -1.2866
111 S V 0.0000
112 Y V -0.6733
113 R V -0.6301
114 G V -0.0425
115 H V 0.0000
116 L V 0.6711
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 -0.0519
123 G V -0.3780
124 T V -0.7008
125 H V -0.8269
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 1.2599
138 P V 0.0000
139 S V 0.5594
140 L V 0.6273
141 N V 0.0244
142 V V 0.5601
143 D V -1.4647
144 G V -1.3281
145 Q V -1.2387
146 P V -0.5699
147 I V 0.6918
148 F V 0.4851
149 A V 0.0000
150 N V -0.9053
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 0.7377
157 T V 0.2308
158 L V 0.6452
159 K V -1.1235
160 E V -1.3089
161 R V -0.7083
162 C V -0.0422
163 L V -0.5064
164 Q V 0.0000
165 V V 0.9368
166 V V 0.9261
167 R V -0.1393
168 S V 0.5486
169 L V 1.4154
170 V V -0.4200
171 K V -2.1605
172 P V -2.5891
173 E V -3.4189
174 N V -3.1130
175 Y V 0.0000
176 R V -3.5185
177 R V -3.2525
178 L V -1.7021
179 D V -1.8843
180 I V -0.0916
181 V V 0.7862
182 R V -1.5578
183 S V -0.8502
184 L V -0.9704
185 Y V 0.0000
186 E V -3.2818
187 D V -2.7618
188 P V 0.0000 mutated: LP188V
189 E V -3.3034
190 D V -3.4199
191 H V -2.8605
192 P V -1.9340
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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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, -0.7826 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 -0.7826 View CSV PDB
model_5 -0.868 View CSV PDB
model_7 -0.9086 View CSV PDB
model_11 -0.9283 View CSV PDB
model_10 -0.9573 View CSV PDB
model_2 -0.9575 View CSV PDB
model_4 -0.9616 View CSV PDB
model_6 -0.9885 View CSV PDB
model_0 -1.0047 View CSV PDB
model_8 -1.0293 View CSV PDB
model_1 -1.0401 View CSV PDB
model_3 -1.0814 View CSV PDB
model_9 -1.1318 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018