Project name: Amyloid precursor protein

Status: done

Started: 2026-04-20 15:30:03
Chain sequence(s) A: GSQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKK
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]                                                (00:00:00)
[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 minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:32)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:03:55)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:03:55)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:03:56)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:03:57)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:03:57)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:00)
Show buried residues
Minimal score value
-2.1476
Maximal score value
5.0151
Average score
1.9317
Total score value
83.0627
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 G A -0.4303
2 S A -0.1986
3 Q A -0.4910
4 K A 0.1404
5 L A 1.8812
6 V A 2.4672
7 F A 2.8093
8 F A 2.5112
9 A A 1.1053
10 E A -0.4971
11 D A -0.6580
12 V A 1.3584
13 G A -0.3751
14 S A -1.1173
15 N A -1.6082
16 K A -1.6134
17 G A -0.1260
18 A A 1.6348
19 I A 3.2675
20 I A 2.9618
21 G A 2.7027
22 L A 4.0197
23 M A 4.4366
24 V A 4.3152
25 G A 3.4349
26 G A 2.6918
27 V A 4.1586
28 V A 4.3782
29 I A 4.3015
30 A A 3.4729
31 T A 3.6286
32 V A 4.5275
33 I A 4.6790
34 V A 5.0151
35 I A 4.6946
36 T A 3.7543
37 L A 3.8913
38 V A 3.0998
39 M A 2.1404
40 L A 1.5954
41 K A -0.7904
42 K A -1.9595
43 K A -2.1476
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, 1.9317 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_5 1.9317 View CSV PDB
input 1.7175 View CSV PDB
model_0 1.5439 View CSV PDB
model_9 1.5143 View CSV PDB
model_8 1.487 View CSV PDB
CABS_average 1.4168 View CSV PDB
model_3 1.4004 View CSV PDB
model_2 1.3788 View CSV PDB
model_1 1.3438 View CSV PDB
model_4 1.318 View CSV PDB
model_7 1.3089 View CSV PDB
model_10 1.2821 View CSV PDB
model_11 1.2589 View CSV PDB
model_6 1.2339 View CSV PDB