Project name: 3333

Status: done

Started: 2021-10-13 20:12:31
Settings
Chain sequence(s) A: LRRFSTMPFMFININN
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]                                                (00:00:00)
[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 A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:04)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:01:53)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:01:54)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:01:54)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:01:54)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:01:54)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:01:54)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:01:55)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:55)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:01:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:55)
Show buried residues
Minimal score value
-1.9396
Maximal score value
4.5214
Average score
1.5311
Total score value
24.4981
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 L A 0.3416
2 R A -1.8321
3 R A -1.2446
4 F A 1.8956
5 S A 2.0513
6 T A 2.4906
7 M A 3.0716
8 P A 1.9556
9 F A 3.3011
10 M A 3.6169
11 F A 4.5214
12 I A 4.0041
13 N A 1.7431
14 I A 1.4359
15 N A -0.9144
16 N A -1.9396
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, 1.5311 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_6 1.5311 View CSV PDB
model_0 1.5155 View CSV PDB
model_9 1.2787 View CSV PDB
model_11 1.2171 View CSV PDB
model_7 1.1688 View CSV PDB
model_1 1.0857 View CSV PDB
model_10 0.9115 View CSV PDB
model_3 0.8868 View CSV PDB
input 0.8628 View CSV PDB
model_4 0.8382 View CSV PDB
model_8 0.7024 View CSV PDB
model_5 0.5147 View CSV PDB
model_2 0.1909 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018