Project name: 4AJY_L101P [mutate: LP101V]

Status: done

Started: 2020-09-18 15:01:40
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 LP101V
Energy difference between WT (input) and mutated protein (by FoldX) 4.64648 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                                                       (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:40)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:23:55)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:23:55)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:23:56)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:23:57)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:23:57)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:23:58)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:23:59)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:23:59)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:24:00)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:24:00)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:24:01)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:24:01)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:24:02)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:24:06)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:24:06)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:24:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:08)
Show buried residues
Minimal score value
-4.2575
Maximal score value
1.7868
Average score
-0.7224
Total score value
-106.9177
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 -1.8504
61 P V -0.9906
62 V V 0.0193
63 L V -0.2155
64 R V -0.4293
65 S V -0.0064
66 V V 0.1922
67 N V -1.0319
68 S V -1.8929
69 R V -3.1478
70 E V -2.7685
71 P V 0.0000
72 S V 0.0000
73 Q V -1.1158
74 V V 0.0000
75 I V 0.3761
76 F V 0.0000
77 C V -0.4167
78 N V 0.0000
79 R V -2.4175
80 S V -1.7568
81 P V -1.8338
82 R V -2.3161
83 V V 0.0000
84 V V 0.0000
85 L V 0.0000
86 P V 0.0000
87 V V 0.0000
88 W V 0.1064
89 L V 0.3340
90 N V 0.0000
91 F V 0.8728
92 D V -1.1686
93 G V -1.3826
94 E V -1.3383
95 P V -0.6821
96 Q V -0.7413
97 P V -0.3844
98 Y V -0.1645
99 P V -0.2697
100 T V -0.5265
101 P V -0.9185 mutated: LP101V
102 P V -0.9742
103 P V -1.5368
104 G V -1.5535
105 T V -1.4281
106 G V -1.2539
107 R V -1.4723
108 R V -1.8393
109 I V 0.0000
110 H V -1.2945
111 S V 0.0000
112 Y V -2.0524
113 R V -1.8633
114 G V 0.0000
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 -0.4265
121 D V 0.0000
122 A V -0.6850
123 G V -0.3211
124 T V -0.0503
125 H V -0.2911
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V -0.2529
130 V V 0.0000
131 N V -0.9878
132 Q V -1.3168
133 T V -0.3927
134 E V 0.0000
135 L V 0.6108
136 F V 0.0000
137 V V 0.6340
138 P V 0.5111
139 S V 0.2444
140 L V 0.9910
141 N V -0.5464
142 V V -0.1249
143 D V -2.0931
144 G V -1.2803
145 Q V 0.0000
146 P V 0.3149
147 I V 1.4467
148 F V 1.7868
149 A V 0.0000
150 N V -0.3137
151 I V 0.0000
152 T V -1.1806
153 L V 0.0000
154 P V -0.1582
155 V V 0.6174
156 Y V 0.4951
157 T V 0.4399
158 L V 0.8931
159 K V -0.9553
160 E V -0.6325
161 R V 0.3834
162 C V 0.7479
163 L V 0.0000
164 Q V 0.0000
165 V V 1.4280
166 V V 1.2105
167 R V -0.0252
168 S V 0.2605
169 L V 1.1905
170 V V 0.0000
171 K V -2.5772
172 P V -2.7386
173 E V -3.7046
174 N V -3.0138
175 Y V 0.0000
176 R V -4.2575
177 R V -3.1762
178 L V -1.0922
179 D V -2.0002
180 I V -0.0459
181 V V 0.3678
182 R V -1.9580
183 S V -1.3787
184 L V -0.9956
185 Y V -2.3366
186 E V -3.4224
187 D V -2.9941
188 L V 0.0000
189 E V -3.2295
190 D V -2.4602
191 H V 0.0000
192 P V -1.6665
193 N V -1.4554
194 V V -0.8569
195 Q V -1.7550
196 K V -2.0207
197 D V -1.5997
198 L V -1.3382
199 E V -2.3671
200 R V -2.7098
201 L V -1.6179
202 T V 0.0000
203 Q V -2.3768
204 E V -2.8130
205 R V -2.1964
206 I V 0.0900
207 A V -0.2584
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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, -0.7224 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_2 -0.7224 View CSV PDB
model_9 -0.7709 View CSV PDB
model_3 -0.7832 View CSV PDB
input -0.7874 View CSV PDB
model_1 -0.8075 View CSV PDB
model_8 -0.8092 View CSV PDB
model_10 -0.8152 View CSV PDB
model_5 -0.8191 View CSV PDB
model_4 -0.8343 View CSV PDB
model_7 -0.8369 View CSV PDB
model_0 -0.8398 View CSV PDB
model_11 -0.9604 View CSV PDB
model_6 -0.9773 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018