Project name: ec7d09327379408

Status: done

Started: 2023-09-25 12:46:35
Settings
Chain sequence(s) D: PCPPGTYIAHLNGLSKCLQQMCDPAMGLRASRNSRTENAVC
input PDB
Selected Chain(s) D
Distance of aggregation 10 Å
FoldX usage No
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 D chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:04:23)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:04:23)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:04:24)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:04:25)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:04:25)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:04:25)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:04:25)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:04:25)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:04:26)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:26)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:04:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:27)
Show buried residues

Minimal score value
-2.0077
Maximal score value
2.1138
Average score
0.0785
Total score value
3.2165

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
77 P D -0.0731
78 C D 0.5919
79 P D 0.1657
80 P D 0.0752
81 G D 0.0000
82 T D 0.0000
83 Y D 1.5282
84 I D 2.1138
85 A D 0.4537
86 H D -0.0832
87 L D 0.3012
88 N D -0.7765
89 G D -0.3367
90 L D 0.5919
91 S D 0.4372
92 K D 0.5474
93 C D 1.8261
94 L D 1.5466
95 Q D -0.3428
97 Q D -0.8445
98 M D 0.4805
99 C D 1.1697
100 D D 0.0000
101 P D 0.4665
102 A D 0.4440
103 M D 0.3820
104 G D 0.2303
105 L D 0.8066
106 R D -0.6667
107 A D -0.1767
108 S D -0.4132
109 R D -1.7169
110 N D -1.2896
112 S D -1.4027
113 R D -2.0077
114 T D -0.9407
115 E D -1.2003
116 N D -0.6477
117 A D 0.0000
118 V D 0.6629
119 C D 1.3141
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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, 0.0785 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_11 0.0785 View CSV PDB
model_4 -0.0883 View CSV PDB
model_6 -0.1176 View CSV PDB
model_10 -0.2112 View CSV PDB
model_0 -0.2191 View CSV PDB
model_7 -0.2533 View CSV PDB
model_1 -0.2811 View CSV PDB
model_8 -0.3006 View CSV PDB
model_5 -0.3741 View CSV PDB
model_3 -0.466 View CSV PDB
model_2 -0.474 View CSV PDB
model_9 -0.6335 View CSV PDB
input -0.8998 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018