Project name: 2000

Status: done

Started: 2020-02-11 03:58:33
Settings
Chain sequence(s) A: LRRFSTAPFAFIDINDVINF
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)
[CRITICAL]   FoldX:    FoldX encountered an error: FoldX didn't produce expected repair files.     
                       Can't continue without it. This is unexpected and could indicate FoldX      
                       issues.                                                                     (00:00:01)
[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                                                (00:00:16)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:04:46)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:47)
[INFO]       Movie:    Creting movie with webm format                                              (00:05:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:52)
Show buried residues

Minimal score value
-1.1914
Maximal score value
4.2997
Average score
2.0945
Total score value
41.8898

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
21 L A 1.6410
22 R A -0.7250
23 R A -1.1914
24 F A 1.6195
25 S A 0.6357
26 T A 0.1265
27 A A 1.2497
28 P A 1.4186
29 F A 3.1359
30 A A 3.7303
31 F A 4.2477
32 I A 4.1584
33 D A 1.8248
34 I A 2.5564
35 N A 0.2013
36 D A 1.4194
37 V A 4.0194
38 I A 4.2997
39 N A 3.4535
40 F A 4.0684
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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, 2.0945 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_1 2.0945 View CSV PDB
model_9 1.844 View CSV PDB
model_0 1.6256 View CSV PDB
model_5 1.5064 View CSV PDB
model_3 1.4548 View CSV PDB
input 1.4342 View CSV PDB
model_7 1.3623 View CSV PDB
model_8 1.1691 View CSV PDB
model_4 1.0499 View CSV PDB
model_11 1.0401 View CSV PDB
model_6 0.8544 View CSV PDB
model_2 0.7803 View CSV PDB
model_10 0.7149 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018