Project name: 1LM8_WT

Status: done

Started: 2020-09-20 09:15:15
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
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]       CABS:     Running CABS flex simulation                                                (00:01:38)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:22)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:19:22)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:19:23)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:19:24)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:19:24)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:19:25)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:19:25)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:19:26)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:19:27)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:19:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:19:28)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:19:28)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:19:29)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:19:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:19:31)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:19:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:32)
Show buried residues
Minimal score value
-3.904
Maximal score value
1.8509
Average score
-0.8705
Total score value
-130.5751
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 -1.8425
61 P V -1.0853
62 V V 0.0000
63 L V -0.5481
64 R V -1.1889
65 S V -1.5705
66 V V 0.0000
67 N V -2.4320
68 S V -2.3537
69 R V -3.4255
70 E V -3.1185
71 P V -2.4072
72 S V 0.0000
73 Q V -1.3779
74 V V 0.0000
75 I V -0.0226
76 F V 0.0000
77 C V -0.5106
78 N V 0.0000
79 R V -2.3073
80 S V -1.5847
81 P V -1.2268
82 R V -1.2905
83 V V -0.5450
84 V V 0.0000
85 L V 0.1634
86 P V 0.0000
87 V V 0.0000
88 W V -0.2025
89 L V 0.0000
90 N V -0.8722
91 F V -0.1192
92 D V -1.6794
93 G V -1.5396
94 E V -1.2325
95 P V -0.8234
96 Q V -0.6347
97 P V -0.1680
98 Y V 0.3296
99 P V -0.0541
100 T V 0.0899
101 L V 0.0000
102 P V -0.7655
103 P V -1.2593
104 G V -1.4130
105 T V -0.8854
106 G V -0.9952
107 R V -1.3477
108 R V -1.9249
109 I V -1.3606
110 H V -1.9844
111 S V 0.0000
112 Y V 0.0000
113 R V -3.0404
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 -0.0230
121 D V 0.0000
122 A V -0.2864
123 G V -0.4358
124 T V -0.7118
125 H V -0.7021
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V 0.5977
130 V V 0.0000
131 N V -1.1956
132 Q V -0.7240
133 T V -0.9584
134 E V -1.1831
135 L V 0.0000
136 F V 0.0000
137 V V 0.0000
138 P V 0.0397
139 S V -0.5549
140 L V 0.0571
141 N V -1.9036
142 V V -1.6090
143 D V -2.6891
144 G V -2.0015
145 Q V -1.5658
146 P V -0.5268
147 I V 1.4581
148 F V 1.8509
149 A V 0.0000
150 N V -0.0952
151 I V 0.0000
152 T V -0.4857
153 L V 0.0000
154 P V 0.1628
155 V V 1.3159
156 Y V 1.1851
157 T V 0.4657
158 L V 0.5874
159 K V -1.0597
160 E V 0.0000
161 R V -0.8002
162 C V -0.3039
163 L V 0.0000
164 Q V 0.0000
165 V V 0.5037
166 V V 0.6501
167 R V -0.8554
168 S V 0.3727
169 L V 1.2660
170 V V -0.4927
171 K V -2.9600
172 P V -3.0949
173 E V -3.6981
174 N V -3.1475
175 Y V 0.0000
176 R V -3.9040
177 R V -3.1367
178 L V -0.6871
179 D V -1.4919
180 I V 1.0259
181 V V 0.8403
182 R V -1.6470
183 S V -1.0208
184 L V -0.7063
185 Y V -1.6063
186 E V -2.9747
187 D V -2.2870
188 L V 0.0000
189 E V -2.7562
190 D V -2.4880
191 H V -2.0093
192 P V -1.6103
193 N V -1.9819
194 V V -1.4273
195 Q V -2.5177
196 K V -3.1494
197 D V 0.0000
198 L V -1.5379
199 E V -3.0158
200 R V -2.8714
201 L V 0.0000
202 T V -1.7937
203 Q V -1.9539
204 E V -2.6659
205 R V -1.8832
206 I V 0.1461
207 A V -0.9092
208 H V -1.9899
209 Q V -2.4566
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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, -0.8705 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_2 -0.8705 View CSV PDB
model_4 -0.9081 View CSV PDB
model_1 -0.9514 View CSV PDB
model_9 -0.9581 View CSV PDB
model_5 -0.9623 View CSV PDB
model_7 -0.9631 View CSV PDB
input -0.9762 View CSV PDB
model_0 -0.9829 View CSV PDB
model_8 -1.0085 View CSV PDB
model_6 -1.015 View CSV PDB
model_11 -1.0183 View CSV PDB
model_10 -1.1357 View CSV PDB
model_3 -1.1447 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018