Project name: pep2_dynamics

Status: done

Started: 2026-05-28 18:03:16
Chain sequence(s) A: LATVYVDVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage No
pH calculations No
alphaCutter usage No
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]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:01:07)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:01:07)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:01:08)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:09)
Show buried residues
Minimal score value
1.1372
Maximal score value
3.5875
Average score
2.6147
Total score value
23.5322
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 L A 2.4756
2 A A 1.3987
3 T A 1.8871
4 V A 3.4353
5 Y A 3.5875
6 V A 3.2685
7 D A 1.1372
8 V A 2.9776
9 L A 3.3647
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D 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 A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, 2.6147 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 A4D Score
model_4 2.6147 View CSV PDB
model_0 2.4801 View CSV PDB
model_2 2.3663 View CSV PDB
model_8 2.3655 View CSV PDB
model_5 2.3423 View CSV PDB
model_3 2.2976 View CSV PDB
model_7 2.2898 View CSV PDB
model_10 2.2846 View CSV PDB
CABS_average 2.2714 View CSV PDB
model_6 2.2456 View CSV PDB
model_11 2.2168 View CSV PDB
model_1 2.0774 View CSV PDB
input 2.0105 View CSV PDB
model_9 1.6762 View CSV PDB