Project name: 1LM8_S65W2 [mutate: SW65V]

Status: done

Started: 2020-09-20 09:34:00
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ
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) 72.737 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                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:46)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:38)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:25)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:26)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:26)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:28)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:28)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:29)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:30)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:31)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:31)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:32)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:33)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:20:34)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:34)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:20:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:35)
Show buried residues
Minimal score value
-4.2126
Maximal score value
1.9529
Average score
-0.7255
Total score value
-108.8246
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 -1.5517
61 P V -0.3898
62 V V 1.1834
63 L V 0.7888
64 R V 0.6505
65 W V 1.5781 mutated: SW65V
66 V V 1.4079
67 N V -0.0873
68 S V -0.6954
69 R V -2.2304
70 E V -2.2981
71 P V -2.0144
72 S V 0.0000
73 Q V -1.4381
74 V V 0.0000
75 I V -0.1003
76 F V 0.0000
77 C V -0.4054
78 N V 0.0000
79 R V -1.4062
80 S V -0.9168
81 P V -0.8253
82 R V -0.7251
83 V V 0.0203
84 V V 0.0000
85 L V 0.2513
86 P V 0.0000
87 V V 0.0000
88 W V 0.0315
89 L V 0.0000
90 N V -0.0398
91 F V -0.1009
92 D V -1.2988
93 G V -1.3518
94 E V -1.9194
95 P V -1.4504
96 Q V -1.0210
97 P V -0.4290
98 Y V 0.5347
99 P V 0.1581
100 T V 0.2558
101 L V 0.0000
102 P V -0.5695
103 P V -0.8185
104 G V -1.1412
105 T V -1.1286
106 G V -1.2268
107 R V -1.5155
108 R V -1.8014
109 I V -0.9790
110 H V -1.4788
111 S V 0.0000
112 Y V -1.3578
113 R V -1.5055
114 G V -0.1400
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 -0.5643
121 D V 0.0000
122 A V -0.2591
123 G V -0.4139
124 T V 0.0000
125 H V -0.0412
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V -0.3946
130 V V 0.0000
131 N V -1.6169
132 Q V -1.4969
133 T V -0.7435
134 E V 0.0000
135 L V 0.5576
136 F V 0.7862
137 V V 1.2879
138 P V 0.0000
139 S V -0.5155
140 L V -1.1282
141 N V -2.0585
142 V V -1.9654
143 D V -2.7200
144 G V -2.0557
145 Q V -2.0483
146 P V -0.7186
147 I V 0.9936
148 F V 1.8144
149 A V 0.0000
150 N V -0.5639
151 I V 0.0000
152 T V -0.7082
153 L V 0.0000
154 P V 0.7099
155 V V 1.9529
156 Y V 1.0460
157 T V 0.6109
158 L V 1.0675
159 K V -0.9568
160 E V -0.3539
161 R V 0.3335
162 C V 0.3146
163 L V 0.0926
164 Q V 0.0000
165 V V 1.0791
166 V V 1.0983
167 R V -0.3405
168 S V 0.5721
169 L V 1.3830
170 V V 0.0000
171 K V -1.9934
172 P V -2.5753
173 E V -3.5931
174 N V -3.0169
175 Y V -2.3373
176 R V -4.2126
177 R V -3.1796
178 L V -1.2794
179 D V -1.3954
180 I V 0.8898
181 V V 0.8860
182 R V -1.5564
183 S V -1.2043
184 L V -0.4729
185 Y V -1.6533
186 E V -2.9966
187 D V -2.3164
188 L V 0.0000
189 E V -3.1362
190 D V -2.5309
191 H V -1.9390
192 P V -1.9529
193 N V -1.8277
194 V V 0.0000
195 Q V -2.3591
196 K V -2.6826
197 D V 0.0000
198 L V 0.0000
199 E V -3.2503
200 R V -3.5499
201 L V -2.2381
202 T V 0.0000
203 Q V -2.9777
204 E V -3.7200
205 R V -2.8976
206 I V -0.7119
207 A V -1.4905
208 H V -2.2070
209 Q V -1.8847
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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, -0.7255 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_3 -0.7255 View CSV PDB
model_6 -0.7905 View CSV PDB
model_2 -0.8079 View CSV PDB
model_7 -0.812 View CSV PDB
model_8 -0.8237 View CSV PDB
model_4 -0.8311 View CSV PDB
model_11 -0.8417 View CSV PDB
model_1 -0.8498 View CSV PDB
model_9 -0.8502 View CSV PDB
model_5 -0.8966 View CSV PDB
model_10 -0.8988 View CSV PDB
model_0 -0.9169 View CSV PDB
input -0.945 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018