Project name: 4AJY_L128H [mutate: LH128V]

Status: done

Started: 2020-09-18 14:43:59
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 LH128V
Energy difference between WT (input) and mutated protein (by FoldX) 2.17809 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                                                       (00:01:48)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:54)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:47)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:28:05)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:28:06)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:28:07)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:28:07)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:28:08)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:28:09)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:28:09)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:28:10)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:28:11)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:28:11)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:28:12)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:28:13)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:28:13)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:28:15)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:28:15)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:28:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:28:16)
Show buried residues
Minimal score value
-3.6961
Maximal score value
2.1393
Average score
-0.6254
Total score value
-92.5619
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 -2.0331
61 P V -1.8641
62 V V 0.0000
63 L V 0.5535
64 R V 0.7912
65 S V 0.9116
66 V V 1.2277
67 N V -0.3330
68 S V -1.0344
69 R V -2.3091
70 E V 0.0000
71 P V -1.4805
72 S V 0.0000
73 Q V -1.3104
74 V V 0.0000
75 I V 1.2475
76 F V 0.0000
77 C V -0.0779
78 N V 0.0000
79 R V -2.3621
80 S V -1.5192
81 P V -1.4907
82 R V -1.5966
83 V V -0.2945
84 V V 0.0000
85 L V 0.3625
86 P V 0.0000
87 V V 0.0000
88 W V -0.1105
89 L V 0.0000
90 N V -0.4394
91 F V -0.2064
92 D V -1.5734
93 G V -1.9065
94 E V -2.1802
95 P V -1.3282
96 Q V -1.0246
97 P V -0.5621
98 Y V -0.0185
99 P V -0.0723
100 T V 0.0000
101 L V 0.0822
102 P V -0.3885
103 P V -1.2243
104 G V -1.3810
105 T V -1.0188
106 G V -0.6647
107 R V -0.8005
108 R V -1.3901
109 I V 0.0000
110 H V -1.5046
111 S V 0.0000
112 Y V -0.3972
113 R V -0.7483
114 G V 0.0000
115 H V 0.0000
116 L V 0.8455
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.2316
121 D V 0.0000
122 A V 0.0000
123 G V -0.1037
124 T V -0.0954
125 H V -0.6373
126 D V -0.8029
127 G V 0.0000
128 H V 0.0000 mutated: LH128V
129 L V -0.5753
130 V V 0.0000
131 N V -1.9363
132 Q V -1.6947
133 T V -0.9231
134 E V -0.4968
135 L V 0.4113
136 F V 0.0000
137 V V 0.6414
138 P V 0.5050
139 S V -0.0431
140 L V 0.0494
141 N V -1.3284
142 V V -1.0403
143 D V -2.2813
144 G V -1.6585
145 Q V 0.0000
146 P V 0.0051
147 I V 0.9136
148 F V 2.1393
149 A V 0.0000
150 N V -0.7993
151 I V 0.0000
152 T V -1.0176
153 L V 0.0000
154 P V 0.1459
155 V V 1.2993
156 Y V 0.7816
157 T V 0.3186
158 L V 0.7285
159 K V -0.9867
160 E V -0.9030
161 R V -0.1772
162 C V 0.4778
163 L V 0.0000
164 Q V 0.0000
165 V V 1.0486
166 V V 1.6608
167 R V 0.0000
168 S V 0.5051
169 L V 1.8716
170 V V 0.9740
171 K V -1.5031
172 P V -1.9278
173 E V -3.3247
174 N V -2.4124
175 Y V 0.0000
176 R V -3.6884
177 R V -2.9557
178 L V -0.1547
179 D V -0.7794
180 I V 1.5257
181 V V 1.4609
182 R V -1.6307
183 S V -0.9410
184 L V -0.9382
185 Y V -2.0306
186 E V -2.9376
187 D V -2.3083
188 L V 0.0000
189 E V -2.9213
190 D V -2.0644
191 H V -2.0363
192 P V 0.0000
193 N V -1.7517
194 V V -1.4810
195 Q V -2.4724
196 K V -2.4166
197 D V 0.0000
198 L V 0.0000
199 E V -3.6961
200 R V -3.1985
201 L V -1.8296
202 T V -2.3541
203 Q V -2.7402
204 E V -3.0121
205 R V -2.3262
206 I V 0.2376
207 A V -0.0734
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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, -0.6254 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_0 -0.6254 View CSV PDB
model_4 -0.6737 View CSV PDB
model_7 -0.7022 View CSV PDB
model_2 -0.7375 View CSV PDB
model_5 -0.7519 View CSV PDB
model_3 -0.7591 View CSV PDB
input -0.7867 View CSV PDB
model_9 -0.8027 View CSV PDB
model_6 -0.8263 View CSV PDB
model_11 -0.8481 View CSV PDB
model_10 -0.8581 View CSV PDB
model_8 -0.8598 View CSV PDB
model_1 -0.8877 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018