Project name: 4AJY_S65W3 [mutate: SW65V]

Status: done

Started: 2020-09-20 09:51:43
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 SW65V
Energy difference between WT (input) and mutated protein (by FoldX) 75.7857 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             (00:00:01)
[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                                                       (00:01:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:45)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:43)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:20)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:21)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:21)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:22)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:22)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:23)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:24)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:24)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:25)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:25)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:26)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:27)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:27)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:21:28)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:29)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:21:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:30)
Show buried residues
Minimal score value
-4.1808
Maximal score value
1.9673
Average score
-0.783
Total score value
-115.8778
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 -1.7875
61 P V -0.8549
62 V V 0.8551
63 L V 0.0000
64 R V -1.0734
65 W V 0.0000 mutated: SW65V
66 V V -0.2686
67 N V -1.0492
68 S V -1.3903
69 R V -2.3872
70 E V -1.7058
71 P V -1.1604
72 S V 0.0000
73 Q V -0.9668
74 V V 0.0000
75 I V -0.6857
76 F V 0.0000
77 C V 0.0000
78 N V 0.0000
79 R V -2.2267
80 S V 0.0000
81 P V -0.6082
82 R V -0.1399
83 V V 0.7862
84 V V 0.0000
85 L V 0.2547
86 P V 0.0000
87 V V 0.0000
88 W V -0.2441
89 L V 0.0000
90 N V -1.2506
91 F V -1.1258
92 D V -2.4798
93 G V -1.9434
94 E V -2.7689
95 P V -1.5937
96 Q V -0.9112
97 P V -0.1714
98 Y V 0.3579
99 P V 0.0185
100 T V 0.1858
101 L V 0.0000
102 P V -0.3017
103 P V -0.7634
104 G V -1.2364
105 T V -0.9910
106 G V -1.4677
107 R V -1.5582
108 R V -2.1536
109 I V -1.2635
110 H V -1.2967
111 S V 0.0000
112 Y V -0.6681
113 R V -0.6120
114 G V -0.0157
115 H V 0.0000
116 L V 0.7068
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V 0.0000
121 D V 0.0000
122 A V -0.0518
123 G V -0.3779
124 T V -0.7001
125 H V -0.8268
126 D V 0.0000
127 G V -0.2436
128 L V 0.0000
129 L V -0.0779
130 V V 0.0000
131 N V -1.0640
132 Q V -1.4160
133 T V -0.8652
134 E V -0.6022
135 L V 0.2045
136 F V 0.0000
137 V V 1.3808
138 P V 0.0000
139 S V 0.5883
140 L V 0.6248
141 N V 0.0235
142 V V 0.5601
143 D V -1.4647
144 G V -1.3281
145 Q V -1.2387
146 P V -0.5720
147 I V 0.7049
148 F V 0.4851
149 A V 0.0000
150 N V -0.9053
151 I V 0.0000
152 T V -0.5853
153 L V 0.5084
154 P V 0.9404
155 V V 1.9673
156 Y V 0.7472
157 T V 0.2307
158 L V 0.6471
159 K V -1.1223
160 E V -1.3464
161 R V -0.7389
162 C V -0.0975
163 L V 0.0000
164 Q V 0.0000
165 V V 0.8741
166 V V 0.8341
167 R V -0.1965
168 S V 0.5148
169 L V 1.3861
170 V V -0.4311
171 K V -2.1651
172 P V -2.5907
173 E V -3.4167
174 N V -3.1105
175 Y V 0.0000
176 R V -3.5327
177 R V -3.2525
178 L V -1.7122
179 D V -1.8946
180 I V -0.1124
181 V V 0.7769
182 R V -1.5909
183 S V -0.9012
184 L V -1.0481
185 Y V 0.0000
186 E V -3.4497
187 D V -2.8860
188 L V 0.0000
189 E V -3.3808
190 D V -3.4846
191 H V -2.9026
192 P V -1.9334
193 N V -2.1483
194 V V -1.8169
195 Q V -3.0216
196 K V -3.2969
197 D V -2.7504
198 L V 0.0000
199 E V -4.1016
200 R V -4.1808
201 L V -2.5120
202 T V -1.9447
203 Q V -2.5858
204 E V -2.9483
205 R V -1.5502
206 I V 0.7955
207 A V -0.2414
Download PDB file
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, -0.783 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
input -0.783 View CSV PDB
model_4 -0.925 View CSV PDB
model_2 -0.9409 View CSV PDB
model_11 -0.9416 View CSV PDB
model_9 -0.9575 View CSV PDB
model_8 -0.971 View CSV PDB
model_5 -0.988 View CSV PDB
model_6 -0.9949 View CSV PDB
model_1 -0.9996 View CSV PDB
model_3 -1.047 View CSV PDB
model_10 -1.0779 View CSV PDB
model_7 -1.1033 View CSV PDB
model_0 -1.1256 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018