Project name: AFP9_Amyloid_Prediction_Aggrescan4D

Status: done

Started: 2026-02-17 21:58:32
Chain sequence(s) A: DTASDAAAAAAATAATAAAAAAATAVTAAKAAALTAANAAAAAAATAAAAAR
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:02)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:13)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/e0054a26318ab17/tmp/folded.pdb                (00:00:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:48)
Show buried residues
Minimal score value
-2.3367
Maximal score value
1.3835
Average score
-0.2065
Total score value
-10.7359
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 D A -2.3367
2 T A -1.5399
3 A A -1.1355
4 S A -1.5759
5 D A -2.2742
6 A A -1.0340
7 A A -0.4860
8 A A -0.5174
9 A A -0.3405
10 A A -0.1082
11 A A -0.0058
12 A A 0.1503
13 T A 0.0740
14 A A 0.1465
15 A A 0.1474
16 T A 0.0765
17 A A 0.1534
18 A A 0.1769
19 A A 0.1716
20 A A 0.3523
21 A A 0.4056
22 A A 0.6204
23 A A 0.7515
24 T A 0.4336
25 A A 0.7167
26 V A 1.3835
27 T A 0.2884
28 A A 0.2454
29 A A 0.0784
30 K A -0.8304
31 A A -0.0644
32 A A 0.0032
33 A A -0.0913
34 L A 0.4389
35 T A -0.0606
36 A A -0.0641
37 A A -0.0407
38 N A -0.8235
39 A A -0.2669
40 A A -0.0944
41 A A -0.2576
42 A A -0.1481
43 A A 0.0092
44 A A 0.0607
45 A A 0.1773
46 T A 0.1058
47 A A -0.0827
48 A A -0.3000
49 A A -0.4692
50 A A -0.4307
51 A A -0.7589
52 R A -1.7658
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is likely a peptide. Results may be inaccurate. The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 1.6809 2.8074 View CSV PDB
4.5 1.642 2.8074 View CSV PDB
5.0 1.5955 2.8074 View CSV PDB
5.5 1.5488 2.8074 View CSV PDB
6.0 1.509 2.8074 View CSV PDB
6.5 1.4802 2.8074 View CSV PDB
7.0 1.4605 2.8074 View CSV PDB
7.5 1.446 2.8074 View CSV PDB
8.0 1.435 2.8074 View CSV PDB
8.5 1.4296 2.8346 View CSV PDB
9.0 1.4336 2.9695 View CSV PDB