Project name: SP2053

Status: done

Started: 2020-02-14 15:45:58
Settings
Chain sequence(s) A: FIDINDVIN
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:04)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:04)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:08)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:22)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:24)
[INFO]       Movie:    Creting movie with webm format                                              (00:03:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:12)
Show buried residues

Minimal score value
-0.6543
Maximal score value
3.2279
Average score
1.5181
Total score value
13.6632

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
31 F A 3.1323
32 I A 3.2279
33 D A 0.9334
34 I A 1.7941
35 N A -0.5986
36 D A -0.6543
37 V A 2.2146
38 I A 2.9659
39 N A 0.6479
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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, 1.5181 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
input 1.5181 View CSV PDB
model_1 1.4168 View CSV PDB
model_8 1.3032 View CSV PDB
model_6 1.2931 View CSV PDB
model_4 1.2825 View CSV PDB
model_3 1.1835 View CSV PDB
model_11 1.0675 View CSV PDB
model_2 1.0499 View CSV PDB
model_5 1.0445 View CSV PDB
model_7 1.0189 View CSV PDB
model_10 0.9216 View CSV PDB
model_0 0.8726 View CSV PDB
model_9 0.8627 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018