Project name: 4AJY_R120G [mutate: RG120V]

Status: done

Started: 2020-09-18 14:44:51
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 RG120V
Energy difference between WT (input) and mutated protein (by FoldX) 3.62546 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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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             (00:00:01)
[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                                                       (00:01:48)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:54)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:08)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:28:55)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:28:56)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:28:56)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:28:57)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:28:58)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:28:58)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:28:59)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:00)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:00)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:01)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:02)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:03)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:03)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:29:05)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:05)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:29:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:06)
Show buried residues

Minimal score value
-4.0938
Maximal score value
2.5234
Average score
-0.7129
Total score value
-105.5055

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 -1.8039
61 P V -0.0821
62 V V 1.5256
63 L V 0.0000
64 R V 0.0366
65 S V -0.0967
66 V V -0.0933
67 N V -1.2972
68 S V -1.4092
69 R V -2.4536
70 E V -1.9386
71 P V -1.5934
72 S V 0.0000
73 Q V -1.3607
74 V V 0.0000
75 I V 0.2504
76 F V 0.0000
77 C V -0.4193
78 N V 0.0000
79 R V -2.2192
80 S V -1.3424
81 P V -1.2753
82 R V -1.0732
83 V V 0.4086
84 V V 0.0000
85 L V 0.7631
86 P V 0.0000
87 V V 0.2129
88 W V -0.0954
89 L V 0.0000
90 N V -0.9536
91 F V 0.1141
92 D V -1.7687
93 G V -1.5366
94 E V -2.3856
95 P V -1.5793
96 Q V -1.0981
97 P V -0.3071
98 Y V 0.3809
99 P V 0.1717
100 T V 0.3376
101 L V 0.0000
102 P V -0.6272
103 P V -1.2150
104 G V -1.3097
105 T V -1.1996
106 G V -1.0999
107 R V 0.0000
108 R V -1.7244
109 I V 0.0000
110 H V -1.5840
111 S V 0.0000
112 Y V -0.3082
113 R V -1.2317
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 G V 0.0000 mutated: RG120V
121 D V 0.0000
122 A V 0.0219
123 G V 0.1437
124 T V -0.0710
125 H V -0.5391
126 D V -0.2022
127 G V 0.1936
128 L V 0.0000
129 L V -0.1117
130 V V 0.0000
131 N V -1.7546
132 Q V -1.8368
133 T V -1.1840
134 E V -1.0243
135 L V 0.0000
136 F V 0.0136
137 V V 0.8414
138 P V 0.7811
139 S V -0.0015
140 L V 0.0340
141 N V -1.7887
142 V V 0.0000
143 D V -2.6640
144 G V -1.8892
145 Q V -1.5448
146 P V -0.6621
147 I V 1.1366
148 F V 1.6612
149 A V 0.0000
150 N V -0.5312
151 I V 0.0000
152 T V -0.7019
153 L V 0.2882
154 P V 1.2473
155 V V 2.5234
156 Y V 1.7968
157 T V 0.6707
158 L V 0.7171
159 K V -1.1230
160 E V -0.9378
161 R V -0.6399
162 C V 0.3728
163 L V 0.3670
164 Q V 0.0000
165 V V 1.9088
166 V V 1.6899
167 R V 0.0000
168 S V 0.6945
169 L V 1.6797
170 V V 0.0000
171 K V -2.6272
172 P V -2.5257
173 E V -3.7800
174 N V -2.8730
175 Y V 0.0000
176 R V -4.0938
177 R V -3.2247
178 L V -1.2116
179 D V -1.4963
180 I V 0.4030
181 V V 0.2409
182 R V -1.9505
183 S V -1.3821
184 L V -1.0558
185 Y V -2.1810
186 E V -3.1955
187 D V -2.7463
188 L V 0.0000
189 E V -3.1299
190 D V -3.1376
191 H V -2.2489
192 P V -2.0960
193 N V -2.0456
194 V V -1.1814
195 Q V -2.3100
196 K V -2.8979
197 D V -2.3022
198 L V 0.0000
199 E V -3.8995
200 R V -3.6343
201 L V -2.5620
202 T V 0.0000
203 Q V -2.2320
204 E V -2.7051
205 R V -1.2490
206 I V 0.7644
207 A V -0.2337
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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, -0.7129 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_8 -0.7129 View CSV PDB
input -0.8006 View CSV PDB
model_11 -0.8008 View CSV PDB
model_7 -0.805 View CSV PDB
model_1 -0.8476 View CSV PDB
model_10 -0.8503 View CSV PDB
model_0 -0.8741 View CSV PDB
model_5 -0.8766 View CSV PDB
model_3 -0.886 View CSV PDB
model_9 -0.8933 View CSV PDB
model_6 -0.9001 View CSV PDB
model_2 -0.9154 View CSV PDB
model_4 -0.9855 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018