Project name: 4AJY_W88R [mutate: WR88V]

Status: done

Started: 2020-09-18 14:41:09
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 WR88V
Energy difference between WT (input) and mutated protein (by FoldX) 1.88933 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]                                                (00:00:01)
[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                                                       (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:44)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:38)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:27:24)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:27:25)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:27:26)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:27:27)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:27:27)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:27:28)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:27:29)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:27:30)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:27:30)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:27:31)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:27:32)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:27:33)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:27:33)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:27:35)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:27:35)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:27:35)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:36)
Show buried residues
Minimal score value
-4.1302
Maximal score value
1.7526
Average score
-0.7728
Total score value
-114.3774
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 -0.9528
61 P V -0.1273
62 V V 1.5900
63 L V 1.1063
64 R V 0.0000
65 S V 1.1000
66 V V 0.9645
67 N V -0.8259
68 S V -1.4516
69 R V -2.7780
70 E V -3.0278
71 P V -2.5430
72 S V 0.0000
73 Q V -1.6423
74 V V 0.0000
75 I V -0.4304
76 F V 0.0000
77 C V -0.8830
78 N V 0.0000
79 R V -2.2426
80 S V -1.2046
81 P V -0.8211
82 R V 0.0000
83 V V -0.1254
84 V V 0.0000
85 L V 0.1934
86 P V 0.0000
87 V V -0.1038
88 R V -0.2551 mutated: WR88V
89 L V 0.0865
90 N V 0.0000
91 F V 1.7526
92 D V 0.3961
93 G V -0.2756
94 E V -0.5630
95 P V -0.5700
96 Q V -0.7745
97 P V -0.4146
98 Y V -0.2464
99 P V -0.6720
100 T V -0.1722
101 L V 0.0000
102 P V -0.7336
103 P V -0.9803
104 G V -1.4210
105 T V -1.4328
106 G V -1.6796
107 R V -2.5803
108 R V -2.5687
109 I V 0.0000
110 H V -1.8419
111 S V 0.0000
112 Y V 0.0000
113 R V -1.6186
114 G V -0.5891
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 -0.6070
121 D V 0.0000
122 A V -0.2562
123 G V -0.1148
124 T V -0.0185
125 H V -0.3805
126 D V -0.6399
127 G V -0.4967
128 L V 0.0000
129 L V -0.3767
130 V V 0.0000
131 N V -0.9275
132 Q V -1.5993
133 T V -0.9244
134 E V -0.5864
135 L V -0.0496
136 F V 0.0000
137 V V 0.0542
138 P V -0.2155
139 S V -0.6765
140 L V 0.0000
141 N V -2.3678
142 V V 0.0000
143 D V -2.9300
144 G V -2.1143
145 Q V -1.8938
146 P V -0.8637
147 I V 0.6399
148 F V 1.6638
149 A V 0.0000
150 N V -0.9946
151 I V 0.0000
152 T V -0.9501
153 L V 0.0000
154 P V 0.1213
155 V V 0.9062
156 Y V 0.6429
157 T V 0.3511
158 L V 0.7639
159 K V -0.8386
160 E V -0.6469
161 R V -0.1596
162 C V 0.3356
163 L V 0.0000
164 Q V 0.0000
165 V V 1.0053
166 V V 0.7951
167 R V 0.0000
168 S V 0.5516
169 L V 1.2781
170 V V -0.2626
171 K V -2.1312
172 P V -2.3928
173 E V -2.8487
174 N V -2.5193
175 Y V 0.0000
176 R V -3.8773
177 R V -3.0234
178 L V -1.0792
179 D V -1.8587
180 I V -0.2904
181 V V 0.5624
182 R V -1.7431
183 S V -1.3616
184 L V 0.0000
185 Y V -1.7987
186 E V -2.7580
187 D V -2.2532
188 L V 0.0000
189 E V -3.2092
190 D V -2.5155
191 H V -1.7600
192 P V -1.9275
193 N V -2.2783
194 V V -2.2543
195 Q V -2.8033
196 K V -3.2873
197 D V -3.2227
198 L V 0.0000
199 E V -3.7645
200 R V -4.1302
201 L V -2.4169
202 T V 0.0000
203 Q V -2.6937
204 E V -2.8048
205 R V -1.8166
206 I V 0.3533
207 A V -0.3307
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View in 3Dmol
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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, -0.7728 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_4 -0.7728 View CSV PDB
model_10 -0.7894 View CSV PDB
input -0.8023 View CSV PDB
model_1 -0.8352 View CSV PDB
model_3 -0.8506 View CSV PDB
model_8 -0.8568 View CSV PDB
model_2 -0.8687 View CSV PDB
model_5 -0.898 View CSV PDB
model_9 -0.8989 View CSV PDB
model_11 -0.9034 View CSV PDB
model_0 -0.9298 View CSV PDB
model_7 -1.005 View CSV PDB
model_6 -1.0183 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018