Project name: 7d3d28afc2c5541

Status: done

Started: 2021-10-13 19:55:49
Settings
Chain sequence(s) A: FIDINDVINF
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                                                (00:00:02)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:01:22)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:01:23)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:01:23)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:01:23)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:23)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:01:23)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:24)
Show buried residues

Minimal score value
-0.1154
Maximal score value
3.0504
Average score
1.9002
Total score value
19.0021

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
1 F A 2.6172
2 I A 3.0504
3 D A 0.6999
4 I A 1.7345
5 N A -0.1154
6 D A 1.2547
7 V A 2.8041
8 I A 2.9483
9 N A 1.4536
10 F A 2.5548
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View in 3Dmol
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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, 1.9002 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 1.9002 View CSV PDB
model_7 1.5888 View CSV PDB
model_8 1.5712 View CSV PDB
model_10 1.5499 View CSV PDB
model_4 1.4575 View CSV PDB
model_3 1.4492 View CSV PDB
model_9 1.3806 View CSV PDB
model_5 1.3068 View CSV PDB
model_11 1.2466 View CSV PDB
model_6 1.0851 View CSV PDB
model_1 1.0651 View CSV PDB
model_0 1.0589 View CSV PDB
input 1.0469 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018