Project name: 1LM8_WT2

Status: done

Started: 2020-09-20 09:15:55
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]                                                (00:00:00)
[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]       CABS:     Running CABS flex simulation                                                (00:01:36)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:03)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:05)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:06)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:06)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:07)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:08)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:08)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:09)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:10)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:10)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:11)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:20:12)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:13)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:20:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:14)
Show buried residues

Minimal score value
-4.3066
Maximal score value
2.1543
Average score
-0.7536
Total score value
-113.038

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 -1.8285
61 P V -0.7421
62 V V 0.3716
63 L V 0.0000
64 R V -1.6436
65 S V 0.0000
66 V V 0.1562
67 N V -1.5117
68 S V -1.7745
69 R V -2.6853
70 E V -2.3908
71 P V -2.1957
72 S V 0.0000
73 Q V -1.4577
74 V V 0.0000
75 I V -0.4442
76 F V 0.0000
77 C V -0.8408
78 N V 0.0000
79 R V -2.3853
80 S V -1.3832
81 P V 0.0000
82 R V -2.0400
83 V V -0.8974
84 V V 0.0000
85 L V 0.1431
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.0000
90 N V -1.3274
91 F V -1.6508
92 D V -2.4121
93 G V -2.3769
94 E V -2.4200
95 P V -1.7323
96 Q V -0.8684
97 P V -0.4759
98 Y V -0.0507
99 P V -0.4198
100 T V -0.0386
101 L V 0.0000
102 P V -1.0925
103 P V -1.5348
104 G V -1.5441
105 T V -1.3007
106 G V -1.5774
107 R V -1.9441
108 R V -2.3072
109 I V 0.0000
110 H V -1.9464
111 S V 0.0000
112 Y V 0.0000
113 R V -2.0829
114 G V -0.8128
115 H V 0.0000
116 L V 0.5641
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.4020
121 D V 0.0000
122 A V -0.5091
123 G V -0.3452
124 T V -0.1534
125 H V -0.2819
126 D V 0.0000
127 G V -0.3453
128 L V 0.0000
129 L V -0.1889
130 V V 0.0000
131 N V -1.6879
132 Q V -1.7761
133 T V -0.8657
134 E V -0.6475
135 L V 0.1967
136 F V 1.1309
137 V V 2.1543
138 P V 0.0000
139 S V -0.1226
140 L V 0.1120
141 N V -0.6882
142 V V 0.1247
143 D V -1.3896
144 G V -1.2154
145 Q V 0.0000
146 P V -0.4593
147 I V 0.0000
148 F V 1.7318
149 A V 0.0000
150 N V -0.9187
151 I V 0.0000
152 T V -0.7568
153 L V 0.0000
154 P V 0.2012
155 V V 2.0330
156 Y V 1.2562
157 T V 0.7552
158 L V 0.9840
159 K V -0.6669
160 E V -0.4484
161 R V 0.0413
162 C V 0.3929
163 L V 0.0000
164 Q V 0.0000
165 V V 1.2142
166 V V 1.1567
167 R V 0.0397
168 S V 0.6794
169 L V 1.4722
170 V V -0.4294
171 K V -2.5995
172 P V -2.7604
173 E V -3.4541
174 N V -2.8720
175 Y V 0.0000
176 R V -4.3066
177 R V -3.3970
178 L V -1.3260
179 D V -2.0777
180 I V -0.7264
181 V V 0.4922
182 R V -1.9542
183 S V -1.1926
184 L V -1.1001
185 Y V -2.1822
186 E V -3.1745
187 D V -2.4845
188 L V 0.0000
189 E V -3.1001
190 D V -2.6840
191 H V -2.3975
192 P V 0.0000
193 N V -1.6772
194 V V 0.0000
195 Q V -1.9568
196 K V -1.9822
197 D V 0.0000
198 L V 0.0000
199 E V -2.0849
200 R V -1.9884
201 L V 0.0000
202 T V 0.0000
203 Q V -1.4079
204 E V -1.5845
205 R V -1.4693
206 I V 0.1113
207 A V -0.7359
208 H V -1.7205
209 Q V -1.7210
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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, -0.7536 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 -0.7536 View CSV PDB
model_11 -0.7682 View CSV PDB
model_4 -0.7868 View CSV PDB
model_10 -0.7881 View CSV PDB
model_8 -0.8459 View CSV PDB
model_2 -0.8476 View CSV PDB
model_1 -0.8773 View CSV PDB
model_5 -0.8847 View CSV PDB
model_7 -0.9001 View CSV PDB
model_6 -0.9077 View CSV PDB
model_3 -0.9124 View CSV PDB
model_9 -0.9236 View CSV PDB
input -0.9762 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018