Project name: abeta3

Status: done

Started: 2026-03-03 10:50:36
Chain sequence(s) A: LVFFAEDVGSNKGAIIGLMVGGVV
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
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]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:15)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:01:59)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:01)
Show buried residues
Minimal score value
-1.6419
Maximal score value
4.3084
Average score
1.7642
Total score value
42.3409
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 2.8826
2 V A 3.7750
3 F A 3.3719
4 F A 3.0667
5 A A 1.7355
6 E A -0.4484
7 D A -0.7198
8 V A 0.3711
9 G A -1.0925
10 S A -1.3193
11 N A -1.6419
12 K A -1.1934
13 G A 0.2013
14 A A 1.2710
15 I A 2.9958
16 I A 3.5060
17 G A 2.5318
18 L A 3.7223
19 M A 4.3084
20 V A 4.1720
21 G A 2.3704
22 G A 2.2687
23 V A 3.2921
24 V A 2.9136
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, 1.7642 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_3 1.7642 View CSV PDB
model_0 1.6806 View CSV PDB
model_6 1.6372 View CSV PDB
model_9 1.6122 View CSV PDB
model_4 1.5598 View CSV PDB
model_7 1.5477 View CSV PDB
model_5 1.5442 View CSV PDB
CABS_average 1.5346 View CSV PDB
model_10 1.5012 View CSV PDB
model_11 1.464 View CSV PDB
model_2 1.4469 View CSV PDB
input 1.4292 View CSV PDB
model_1 1.3846 View CSV PDB
model_8 1.2734 View CSV PDB