Project name: 4AJY_V165D [mutate: VD165V]

Status: done

Started: 2020-09-18 14:31:21
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 VD165V
Energy difference between WT (input) and mutated protein (by FoldX) 0.503826 kcal/mol
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                                        (00:01:54)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:45)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:29:16)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:17)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:29:18)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:19)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:29:19)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:20)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:29:20)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:21)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:29:22)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:23)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:29:23)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:29:24)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:25)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:29:28)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:28)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:29:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:29)
Show buried residues
Minimal score value
-3.8677
Maximal score value
1.6987
Average score
-0.764
Total score value
-113.0768
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 -2.0232
61 P V -0.9524
62 V V 0.6957
63 L V -0.0640
64 R V -0.5819
65 S V 0.1640
66 V V 0.7921
67 N V -0.5840
68 S V -1.3225
69 R V -2.6632
70 E V -3.0188
71 P V -2.2188
72 S V 0.0000
73 Q V -1.5125
74 V V 0.0000
75 I V 0.2829
76 F V 0.0000
77 C V -0.2837
78 N V 0.0000
79 R V -2.0895
80 S V -1.4148
81 P V -1.3682
82 R V -1.8532
83 V V -0.5890
84 V V 0.0000
85 L V 0.1074
86 P V 0.0000
87 V V 0.1935
88 W V 0.0000
89 L V -0.3511
90 N V 0.0000
91 F V 0.2146
92 D V -1.5837
93 G V -1.6918
94 E V -2.1755
95 P V -1.1309
96 Q V -0.9478
97 P V -0.4068
98 Y V 0.0683
99 P V -0.0312
100 T V -0.1498
101 L V 0.0000
102 P V -0.9764
103 P V -1.4327
104 G V -1.1311
105 T V -1.1268
106 G V -1.4155
107 R V -1.8997
108 R V -2.0964
109 I V 0.0000
110 H V -1.7143
111 S V 0.0000
112 Y V -0.9788
113 R V -1.1868
114 G V -0.0182
115 H V 0.0000
116 L V 0.3805
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.2895
121 D V 0.0000
122 A V -0.5541
123 G V -0.7272
124 T V 0.0000
125 H V -0.7014
126 D V 0.0000
127 G V 0.0859
128 L V 0.0000
129 L V -0.3285
130 V V 0.0000
131 N V -1.5485
132 Q V -1.6156
133 T V -0.9494
134 E V -0.5102
135 L V -0.1140
136 F V 0.0000
137 V V 0.6637
138 P V 0.2589
139 S V -0.4225
140 L V -0.4740
141 N V -2.0384
142 V V -1.7279
143 D V -2.8125
144 G V -2.0518
145 Q V -1.7528
146 P V -0.7185
147 I V 0.6984
148 F V 1.6987
149 A V 0.0000
150 N V -0.6111
151 I V 0.0000
152 T V -0.4361
153 L V 0.8392
154 P V 1.1440
155 V V 0.9347
156 Y V 0.3509
157 T V 0.1668
158 L V 0.5386
159 K V -1.4572
160 E V -1.3718
161 R V -0.7403
162 C V -0.0282
163 L V -0.2184
164 Q V 0.0000
165 D V -0.6661 mutated: VD165V
166 V V 0.4855
167 R V 0.0000
168 S V -0.2257
169 L V 0.9244
170 V V -0.1095
171 K V -2.2488
172 P V -2.3801
173 E V -3.5417
174 N V -3.0086
175 Y V 0.0000
176 R V -3.8677
177 R V -3.5578
178 L V -1.8980
179 D V -1.5734
180 I V 0.7111
181 V V 0.3189
182 R V -1.6754
183 S V -0.9080
184 L V -0.5626
185 Y V -1.5237
186 E V -2.6042
187 D V -2.3896
188 L V 0.0000
189 E V -2.3652
190 D V -1.8138
191 H V -1.6177
192 P V 0.0000
193 N V -1.2025
194 V V -0.9326
195 Q V -1.9618
196 K V -1.9135
197 D V 0.0000
198 L V 0.0000
199 E V -2.3561
200 R V -2.4199
201 L V 0.0000
202 T V 0.0000
203 Q V -2.3764
204 E V -2.9465
205 R V -2.0577
206 I V 0.2655
207 A V -0.1715
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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, -0.764 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_7 -0.764 View CSV PDB
model_4 -0.8402 View CSV PDB
model_11 -0.8528 View CSV PDB
input -0.8798 View CSV PDB
model_10 -0.8871 View CSV PDB
model_6 -0.8919 View CSV PDB
model_1 -0.8963 View CSV PDB
model_3 -0.9115 View CSV PDB
model_0 -0.9183 View CSV PDB
model_9 -0.9699 View CSV PDB
model_5 -1.0145 View CSV PDB
model_8 -1.0199 View CSV PDB
model_2 -1.0336 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018