Project name: 1LM8_S65W3 [mutate: SW65V]

Status: done

Started: 2020-09-20 09:34:40
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                                         (00:00:01)
[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                                                (00:02:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:02)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:03)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:04)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:04)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:05)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:06)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:06)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:07)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:08)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:08)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:09)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:09)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:10)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:21:11)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:12)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:21:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:13)
Show buried residues
Minimal score value
-4.131
Maximal score value
2.3998
Average score
-0.7617
Total score value
-114.2614
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 -1.8749
61 P V -1.2487
62 V V -0.9307
63 L V -0.6073
64 R V -1.0625
65 W V -0.1404 mutated: SW65V
66 V V -0.3933
67 N V -1.2427
68 S V -1.4686
69 R V -2.4035
70 E V -1.8945
71 P V -1.7117
72 S V 0.0000
73 Q V -1.2450
74 V V 0.0000
75 I V -0.5008
76 F V 0.0000
77 C V -0.7842
78 N V -0.9659
79 R V -1.1757
80 S V -0.6944
81 P V -1.0124
82 R V -0.8577
83 V V -0.3081
84 V V 0.0000
85 L V -0.0580
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V -0.6454
90 N V 0.0000
91 F V 0.1683
92 D V -1.6094
93 G V -1.5307
94 E V -2.2240
95 P V -1.3148
96 Q V -1.3601
97 P V -0.8611
98 Y V 0.0000
99 P V -0.2968
100 T V -0.0197
101 L V 0.0000
102 P V -0.6907
103 P V -1.0045
104 G V -1.0539
105 T V -1.1404
106 G V -1.4386
107 R V -1.8213
108 R V -2.0971
109 I V -1.0906
110 H V -1.5185
111 S V 0.0000
112 Y V -0.4747
113 R V -1.8550
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 -1.0555
121 D V 0.0000
122 A V -0.4709
123 G V -0.5921
124 T V 0.0000
125 H V -0.6683
126 D V 0.0000
127 G V 0.1238
128 L V 0.0000
129 L V 0.3075
130 V V 0.0000
131 N V -0.9466
132 Q V -1.1630
133 T V -0.6252
134 E V -0.5134
135 L V 0.0000
136 F V 0.0000
137 V V 0.7162
138 P V 0.0000
139 S V 0.0242
140 L V -0.6138
141 N V -1.9654
142 V V -1.8512
143 D V -2.4061
144 G V -1.9988
145 Q V -1.6582
146 P V -0.9851
147 I V 0.3638
148 F V 0.9452
149 A V 0.0000
150 N V -0.4129
151 I V 0.0000
152 T V 0.2397
153 L V 1.5867
154 P V 1.5954
155 V V 2.3998
156 Y V 1.2913
157 T V 0.8997
158 L V 1.0754
159 K V -0.8085
160 E V 0.0000
161 R V 0.5398
162 C V 0.8017
163 L V 0.6216
164 Q V 0.0000
165 V V 1.4925
166 V V 1.8773
167 R V 0.0000
168 S V 0.4082
169 L V 1.6163
170 V V -0.1607
171 K V -2.2290
172 P V -2.7798
173 E V -3.9912
174 N V -3.4908
175 Y V 0.0000
176 R V -4.1310
177 R V -3.3984
178 L V -1.0335
179 D V -1.3325
180 I V 1.3577
181 V V 1.0057
182 R V -1.2789
183 S V -0.8034
184 L V -0.2745
185 Y V -1.6421
186 E V -2.3177
187 D V -1.9921
188 L V 0.0000
189 E V -2.7862
190 D V -1.8681
191 H V -2.0181
192 P V 0.0000
193 N V -1.8769
194 V V -1.4178
195 Q V -2.2072
196 K V -2.3100
197 D V 0.0000
198 L V -2.3451
199 E V -3.7659
200 R V -3.6051
201 L V -2.3951
202 T V 0.0000
203 Q V -2.9991
204 E V -3.1003
205 R V -2.0757
206 I V -0.4080
207 A V -0.9852
208 H V -1.7727
209 Q V -1.5638
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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, -0.7617 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 -0.7617 View CSV PDB
model_4 -0.7923 View CSV PDB
model_6 -0.844 View CSV PDB
model_5 -0.8625 View CSV PDB
model_1 -0.8671 View CSV PDB
model_7 -0.8708 View CSV PDB
model_11 -0.8763 View CSV PDB
model_9 -0.9069 View CSV PDB
model_2 -0.9242 View CSV PDB
model_3 -0.9301 View CSV PDB
model_10 -0.9428 View CSV PDB
input -0.945 View CSV PDB
model_8 -0.9905 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018