Project name: cluster4

Status: done

Started: 2026-06-02 11:09:26
Chain sequence(s) A: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
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]                                                (00:00:01)
[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)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:24)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/620447c5ac3a72b/tmp/folded.pdb                (00:00:24)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:47)
Show buried residues
Minimal score value
-2.8489
Maximal score value
3.7243
Average score
0.1479
Total score value
6.2133
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 -2.1210
2 A A -1.2685
3 E A -1.8031
4 F A -0.4488
5 R A -2.6033
6 H A -2.6474
7 D A -2.8489
8 S A -1.8010
9 G A -1.6018
10 Y A -1.0992
11 E A -1.5779
12 V A -0.1925
13 H A -1.3153
14 H A -2.2739
15 Q A -2.1318
16 K A -2.1643
17 L A 2.8723
18 V A 3.7243
19 F A 3.5432
20 F A 2.3870
21 A A 1.1452
22 E A -0.9278
23 D A -1.2065
24 V A 1.0919
25 G A 1.3366
26 S A 1.2348
27 N A -0.1178
28 K A -1.4772
29 G A -0.5066
30 A A 1.0158
31 I A 2.8359
32 I A 2.4343
33 G A 1.1491
34 L A 1.4874
35 M A 0.4782
36 V A 1.8892
37 G A 1.1236
38 G A 1.3220
39 V A 2.4678
40 V A 2.5712
41 I A 1.7209
42 A A 0.5172
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 0.6935 7.5439 View CSV PDB
4.5 0.5984 7.4669 View CSV PDB
5.0 0.4799 7.3543 View CSV PDB
5.5 0.3719 7.2239 View CSV PDB
6.0 0.2976 7.0933 View CSV PDB
6.5 0.2586 6.9781 View CSV PDB
7.0 0.2405 6.8886 View CSV PDB
7.5 0.2276 6.8211 View CSV PDB
8.0 0.2139 6.7655 View CSV PDB
8.5 0.201 6.7157 View CSV PDB
9.0 0.193 6.6714 View CSV PDB