Project name: 4AJY_G93V [mutate: GV93V]

Status: done

Started: 2020-09-18 14:49:41
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 GV93V
Energy difference between WT (input) and mutated protein (by FoldX) 10.1965 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                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:51)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:57)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:56)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:28:24)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:28:24)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:28:25)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:28:26)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:28:26)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:28:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:28:27)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:28:28)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:28:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:28:30)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:28:30)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:28:33)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:28:34)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:28:39)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:28:39)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:28:39)
[INFO]       Main:     Simulation completed successfully.                                          (00:28:40)
Show buried residues
Minimal score value
-4.1745
Maximal score value
1.9664
Average score
-0.777
Total score value
-114.9914
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 -1.7469
61 P V -0.7479
62 V V 0.8971
63 L V 0.0000
64 R V -1.0360
65 S V 0.0000
66 V V -0.4555
67 N V -1.2242
68 S V -1.4877
69 R V -2.4346
70 E V -1.7048
71 P V -1.1515
72 S V 0.0000
73 Q V -0.9623
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 -0.1399
83 V V 0.7862
84 V V 0.0000
85 L V 0.2490
86 P V 0.0000
87 V V 0.0000
88 W V -0.1624
89 L V 0.0000
90 N V -1.1128
91 F V -1.0181
92 D V -2.2828
93 V V -1.5676 mutated: GV93V
94 E V -2.4464
95 P V -1.3980
96 Q V -0.7537
97 P V -0.1526
98 Y V 0.3184
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 -1.2863
111 S V 0.0000
112 Y V -0.7159
113 R V -0.6880
114 G V -0.1372
115 H V 0.0000
116 L V 0.6666
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 -0.2471
128 L V 0.0000
129 L V -0.0852
130 V V 0.0000
131 N V -1.0665
132 Q V -1.4198
133 T V -0.8734
134 E V -0.6202
135 L V 0.1733
136 F V 0.0000
137 V V 1.2549
138 P V 0.0000
139 S V 0.5550
140 L V 0.6290
141 N V 0.0227
142 V V 0.5607
143 D V -1.4644
144 G V -1.3279
145 Q V -1.2385
146 P V -0.5697
147 I V 0.6921
148 F V 0.4851
149 A V 0.0000
150 N V -0.9056
151 I V 0.0000
152 T V -0.5859
153 L V 0.5078
154 P V 0.9377
155 V V 1.9664
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 -1.8145
195 Q V -3.0006
196 K V -3.2971
197 D V -2.7531
198 L V 0.0000
199 E V -4.0971
200 R V -4.1745
201 L V -2.5023
202 T V -1.9264
203 Q V -2.5699
204 E V -2.9241
205 R V -1.5012
206 I V 0.8191
207 A V -0.2254
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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, -0.777 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 -0.777 View CSV PDB
model_3 -0.8618 View CSV PDB
model_1 -0.9386 View CSV PDB
model_11 -0.9448 View CSV PDB
model_5 -0.9467 View CSV PDB
model_8 -1.0012 View CSV PDB
model_2 -1.0166 View CSV PDB
model_9 -1.0273 View CSV PDB
model_0 -1.0289 View CSV PDB
model_7 -1.0413 View CSV PDB
model_10 -1.0432 View CSV PDB
model_6 -1.0481 View CSV PDB
model_4 -1.0767 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018