Project name: c169b8259e5be5a

Status: done

Started: 2023-09-25 13:59:56
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPEELLLLVSQCS
input PDB
Selected Chain(s) A
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 A 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                                                (00:00:10)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:25)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:25)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:25)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:25)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:27)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:27)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:27)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:28)
Show buried residues

Minimal score value
-2.2718
Maximal score value
4.1704
Average score
0.421
Total score value
10.5261

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
70 T A -0.0808
71 C A 0.0892
72 T A -0.0137
73 H A 0.0935
74 G A 1.8071
75 L A 2.9643
76 Y A 2.7017
77 K A -0.8569
78 R A -2.2161
79 T A -1.9330
80 P A -1.6532
81 R A -1.8623
82 Y A -0.8110
83 P A -1.4084
84 E A -2.2718
85 E A -1.1774
86 L A 1.6096
87 L A 3.3573
88 L A 4.1704
89 L A 4.0061
90 V A 3.3059
91 S A 0.9171
92 Q A -0.4050
93 C A 0.2726
94 S A -0.0791
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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, 0.421 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_7 0.421 View CSV PDB
model_9 0.3261 View CSV PDB
model_10 0.2004 View CSV PDB
model_1 0.1252 View CSV PDB
input 0.0969 View CSV PDB
model_8 0.0835 View CSV PDB
model_0 0.0242 View CSV PDB
model_6 -0.0056 View CSV PDB
model_4 -0.0153 View CSV PDB
model_5 -0.0289 View CSV PDB
model_11 -0.0541 View CSV PDB
model_2 -0.0826 View CSV PDB
model_3 -0.2696 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018