Project name: abeta

Status: done

Started: 2026-03-02 21:05:12
Chain sequence(s) A: EVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
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                                                (00:00:58)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:04:35)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:04:35)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:04:36)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:38)
Show buried residues
Minimal score value
-1.9663
Maximal score value
3.6406
Average score
0.9864
Total score value
29.5921
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 E A -1.9663
2 V A -0.3305
3 H A -1.4707
4 H A -1.1306
5 Q A -0.5462
6 K A 0.0567
7 L A 1.6917
8 V A 2.5876
9 F A 2.6645
10 F A 2.5878
11 A A 1.5018
12 E A -0.2016
13 D A -0.3590
14 V A 0.3642
15 G A -1.1711
16 S A -1.4679
17 N A -1.7955
18 K A -1.3157
19 G A -0.0522
20 A A 0.5088
21 I A 2.4258
22 I A 3.0694
23 G A 2.3672
24 L A 3.5265
25 M A 3.6406
26 V A 3.1778
27 G A 2.0595
28 G A 2.1391
29 V A 3.4593
30 V A 3.5711
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, 0.9864 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_0 0.9864 View CSV PDB
model_3 0.9619 View CSV PDB
model_6 0.9247 View CSV PDB
model_9 0.8984 View CSV PDB
model_11 0.8227 View CSV PDB
CABS_average 0.7726 View CSV PDB
model_10 0.7422 View CSV PDB
model_1 0.7196 View CSV PDB
model_4 0.7145 View CSV PDB
model_8 0.6852 View CSV PDB
model_5 0.6647 View CSV PDB
model_2 0.6298 View CSV PDB
model_7 0.5205 View CSV PDB
input 0.5193 View CSV PDB