Project name: 2a143b2fb64bef0

Status: done

Started: 2021-10-13 15:03:32
Settings
Chain sequence(s) A: FDININNINNDF
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                                                (00:00:04)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:17)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:17)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:17)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:17)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:18)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:18)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:19)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:19)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:19)
Show buried residues
Minimal score value
-1.6969
Maximal score value
1.4779
Average score
0.1435
Total score value
1.5784
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
1 F A 1.0381
2 D A 0.1569
3 I A 1.3578
4 N A 0.5500
5 I A 1.4779
6 N A -0.2999
7 N A -0.2247
8 I A 1.0779
9 N A -0.2966
10 N A -1.5621
11 D A -1.6969
Download PDB file
View in 3Dmol
Play the video

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, 0.1435 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 0.1435 View CSV PDB
model_8 0.0184 View CSV PDB
model_9 -0.0396 View CSV PDB
model_10 -0.3029 View CSV PDB
model_0 -0.4575 View CSV PDB
model_4 -0.4797 View CSV PDB
model_1 -0.4853 View CSV PDB
model_11 -0.5071 View CSV PDB
model_3 -0.5515 View CSV PDB
model_5 -0.5726 View CSV PDB
input -0.6769 View CSV PDB
model_2 -0.9087 View CSV PDB
model_6 -0.9829 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018