Project name: 4AJY_R82P [mutate: RP82V]

Status: done

Started: 2020-09-18 15:05:03
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 RP82V
Energy difference between WT (input) and mutated protein (by FoldX) 2.28596 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                                                       (00:01:41)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:51)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:39)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:38)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:40)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:40)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:41)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:41)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:42)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:43)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:44)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:44)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:45)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:46)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:46)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:22:48)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:22:49)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:22:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:50)
Show buried residues
Minimal score value
-3.8546
Maximal score value
1.5952
Average score
-0.7722
Total score value
-114.291
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 -2.1154
61 P V -1.6783
62 V V -0.7556
63 L V 0.0000
64 R V -1.4204
65 S V -0.6910
66 V V -0.5834
67 N V -1.3285
68 S V -1.9108
69 R V -3.2738
70 E V -2.8636
71 P V -2.0067
72 S V 0.0000
73 Q V -1.0593
74 V V 0.0000
75 I V 0.1601
76 F V 0.0000
77 C V -0.5833
78 N V -1.4097
79 R V -2.1343
80 S V -1.1800
81 P V -0.6894
82 P V -0.5388 mutated: RP82V
83 V V -0.3031
84 V V 0.0000
85 L V -0.0740
86 P V 0.0000
87 V V -0.0388
88 W V 0.0000
89 L V 0.0000
90 N V 0.0000
91 F V 0.4876
92 D V -1.3704
93 G V -1.1229
94 E V -0.7433
95 P V -0.4601
96 Q V -0.5957
97 P V -0.3885
98 Y V 0.0000
99 P V -0.3194
100 T V -0.1955
101 L V 0.0000
102 P V -0.6985
103 P V -1.0586
104 G V 0.0000
105 T V -1.1031
106 G V -1.3366
107 R V -1.5971
108 R V -2.0097
109 I V 0.0000
110 H V -1.5003
111 S V 0.0000
112 Y V -1.7447
113 R V -2.0860
114 G V -0.9619
115 H V 0.0000
116 L V 0.4176
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.6584
121 D V 0.0000
122 A V -0.1967
123 G V 0.0697
124 T V 0.0000
125 H V -0.2572
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V 0.0885
130 V V 0.0000
131 N V -1.3502
132 Q V -1.1732
133 T V -0.3233
134 E V 0.0000
135 L V -0.0026
136 F V 0.0000
137 V V 0.4232
138 P V 0.0000
139 S V -0.1507
140 L V -0.6031
141 N V -0.9799
142 V V -0.0994
143 D V -1.6301
144 G V -1.2943
145 Q V -0.8826
146 P V -0.4496
147 I V 0.8781
148 F V 1.5952
149 A V 0.0000
150 N V -0.6780
151 I V 0.0000
152 T V -0.5962
153 L V 0.3535
154 P V 0.7506
155 V V 1.1129
156 Y V 0.6856
157 T V 0.1901
158 L V 0.5455
159 K V -1.1633
160 E V -0.9626
161 R V -0.2894
162 C V 0.1484
163 L V 0.0000
164 Q V 0.0000
165 V V 0.9517
166 V V 0.0000
167 R V 0.0000
168 S V 0.6313
169 L V 1.3182
170 V V -0.4032
171 K V -2.4110
172 P V -2.8684
173 E V -3.3508
174 N V -2.9724
175 Y V 0.0000
176 R V -3.8546
177 R V -2.9096
178 L V -1.0994
179 D V -1.4671
180 I V -0.2661
181 V V 0.6265
182 R V -1.4426
183 S V -1.5686
184 L V -1.2365
185 Y V -2.0759
186 E V -3.1181
187 D V -2.7980
188 L V 0.0000
189 E V -3.4449
190 D V -3.1510
191 H V -2.1925
192 P V 0.0000
193 N V -1.7490
194 V V -0.8925
195 Q V -1.6885
196 K V -2.1409
197 D V 0.0000
198 L V 0.0000
199 E V -2.4742
200 R V -2.4308
201 L V -1.9422
202 T V -2.1247
203 Q V -2.4312
204 E V -2.9496
205 R V -2.2333
206 I V 0.0026
207 A V -0.3690
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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, -0.7722 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_6 -0.7722 View CSV PDB
input -0.8087 View CSV PDB
model_0 -0.809 View CSV PDB
model_1 -0.8197 View CSV PDB
model_3 -0.8236 View CSV PDB
model_2 -0.8385 View CSV PDB
model_7 -0.8496 View CSV PDB
model_4 -0.8764 View CSV PDB
model_8 -0.8846 View CSV PDB
model_11 -0.9025 View CSV PDB
model_5 -0.9171 View CSV PDB
model_10 -0.9528 View CSV PDB
model_9 -0.9564 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018