Project name: cluster3

Status: done

Started: 2026-06-02 11:06:23
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                                          (00:00:19)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2189a2aa37d8a32/tmp/folded.pdb                (00:00:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:40)
Show buried residues
Minimal score value
-2.6918
Maximal score value
3.4722
Average score
0.1969
Total score value
8.269
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 -1.9770
2 A A -1.4482
3 E A -1.7977
4 F A -0.4631
5 R A -2.3969
6 H A -2.5256
7 D A -2.6918
8 S A -1.5456
9 G A -1.2461
10 Y A -0.3452
11 E A -1.6643
12 V A -0.9566
13 H A -1.5894
14 H A -2.3384
15 Q A -1.8129
16 K A -2.0817
17 L A 2.9553
18 V A 3.4722
19 F A 3.3344
20 F A 2.4123
21 A A 1.1780
22 E A -1.1303
23 D A -1.4482
24 V A 1.3235
25 G A 1.6383
26 S A 0.0000
27 N A -0.3611
28 K A -1.6370
29 G A -0.5703
30 A A 0.9456
31 I A 2.0044
32 I A 2.3005
33 G A 0.9328
34 L A 1.9206
35 M A 1.1372
36 V A 1.8729
37 G A 1.2456
38 G A 1.7274
39 V A 3.0676
40 V A 3.0868
41 I A 2.5554
42 A A 1.1856
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 0.5422 6.5774 View CSV PDB
4.5 0.4366 6.5338 View CSV PDB
5.0 0.3133 6.4719 View CSV PDB
5.5 0.2037 6.402 View CSV PDB
6.0 0.1299 6.3351 View CSV PDB
6.5 0.0916 6.2821 View CSV PDB
7.0 0.0759 6.2503 View CSV PDB
7.5 0.0685 6.2361 View CSV PDB
8.0 0.063 6.231 View CSV PDB
8.5 0.0636 6.2293 View CSV PDB
9.0 0.0764 6.2287 View CSV PDB