Project name: 4AJY_R107G [mutate: RG107V]

Status: done

Started: 2020-09-18 14:46:48
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 RG107V
Energy difference between WT (input) and mutated protein (by FoldX) 0.958168 kcal/mol
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                                                       (00:01:51)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:57)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:50)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:29:08)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:29:14)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:16)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:17)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:29:18)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:18)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:29:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:21)
Show buried residues

Minimal score value
-3.7625
Maximal score value
2.3046
Average score
-0.7197
Total score value
-106.5188

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 -2.7757
61 P V -2.0678
62 V V 0.0000
63 L V -1.7182
64 R V -2.1719
65 S V -0.6175
66 V V -0.3078
67 N V -0.9675
68 S V -1.2706
69 R V -2.4270
70 E V -1.7590
71 P V -1.3865
72 S V 0.0000
73 Q V -0.9375
74 V V 0.0000
75 I V 0.5984
76 F V 0.0000
77 C V -0.3053
78 N V 0.0000
79 R V -2.1684
80 S V -1.3199
81 P V -0.9513
82 R V -0.6840
83 V V 0.2756
84 V V 0.0000
85 L V 0.3837
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.0000
90 N V -0.8005
91 F V -0.1786
92 D V -1.6795
93 G V -2.1033
94 E V -2.2601
95 P V -1.7598
96 Q V -1.0063
97 P V -0.3623
98 Y V 0.2473
99 P V 0.1115
100 T V 0.2902
101 L V 0.2844
102 P V -0.3582
103 P V -0.8053
104 G V -1.0985
105 T V -0.6747
106 G V -0.5386
107 G V -0.7775 mutated: RG107V
108 R V -1.3848
109 I V -0.6670
110 H V -1.0267
111 S V 0.0000
112 Y V -0.2312
113 R V -0.9383
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 -0.0926
121 D V 0.0000
122 A V -0.1230
123 G V -0.3485
124 T V -0.2773
125 H V -0.5631
126 D V 0.0000
127 G V 0.2501
128 L V 0.0000
129 L V -0.0366
130 V V 0.0000
131 N V -0.7482
132 Q V -1.5285
133 T V -0.8268
134 E V -0.9112
135 L V 0.0557
136 F V 0.0000
137 V V 0.9670
138 P V 0.0000
139 S V 0.0607
140 L V 0.4950
141 N V -1.4285
142 V V -1.5090
143 D V -2.6458
144 G V -2.1343
145 Q V -1.6276
146 P V -0.3881
147 I V 1.4710
148 F V 1.8993
149 A V 0.0000
150 N V -0.4300
151 I V 0.0000
152 T V -0.7135
153 L V 0.0000
154 P V 0.8830
155 V V 2.3046
156 Y V 1.8095
157 T V 0.6967
158 L V 0.5610
159 K V -1.3456
160 E V -0.9592
161 R V -0.9246
162 C V 0.0007
163 L V 0.0000
164 Q V 0.0000
165 V V 1.5278
166 V V 1.4001
167 R V 0.0000
168 S V 0.7086
169 L V 1.7289
170 V V -0.2593
171 K V -2.5563
172 P V -2.7677
173 E V -3.4307
174 N V -3.0702
175 Y V 0.0000
176 R V -3.7625
177 R V -3.1977
178 L V -1.8354
179 D V -2.1714
180 I V 0.0000
181 V V 0.2347
182 R V -1.9613
183 S V -1.1571
184 L V -1.4606
185 Y V -2.2246
186 E V -3.0021
187 D V -2.6667
188 L V 0.0000
189 E V -3.0884
190 D V -2.3108
191 H V -1.9937
192 P V 0.0000
193 N V -1.4823
194 V V -0.8017
195 Q V -1.9984
196 K V -2.2339
197 D V 0.0000
198 L V 0.0000
199 E V -2.4267
200 R V -2.2990
201 L V 0.0000
202 T V -2.0116
203 Q V -2.4247
204 E V -2.8981
205 R V -2.1304
206 I V 0.0712
207 A V -0.1631
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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, -0.7197 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_5 -0.7197 View CSV PDB
model_4 -0.7334 View CSV PDB
model_9 -0.7421 View CSV PDB
model_1 -0.7469 View CSV PDB
input -0.7755 View CSV PDB
model_7 -0.7786 View CSV PDB
model_0 -0.7888 View CSV PDB
model_10 -0.8039 View CSV PDB
model_3 -0.8437 View CSV PDB
model_8 -0.8494 View CSV PDB
model_2 -0.8648 View CSV PDB
model_11 -0.882 View CSV PDB
model_6 -0.9748 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018