Project name: 604aa2d1c17b942

Status: done

Started: 2025-07-31 13:47:23
Chain sequence(s) A: HHHHHH
C: HHHHHH
B: HHHHHH
D: HHHHHH
input PDB
Selected Chain(s) A,C,B,D
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 all 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                                          (00:00:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/604aa2d1c17b942/tmp/folded.pdb                (00:00:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:07)
Show buried residues
Minimal score value
-2.507
Maximal score value
-2.0054
Average score
-2.2701
Total score value
-54.4814
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 H A -2.1359
2 H A -2.3810
3 H A -2.1871
4 H A -2.2345
5 H A -2.2895
6 H A -2.1618
1 H B -2.2897
2 H B -2.3586
3 H B -2.0622
4 H B -2.0054
5 H B -2.1846
6 H B -2.4825
1 H C -2.4582
2 H C -2.3900
3 H C -2.1519
4 H C -2.0685
5 H C -2.2162
6 H C -2.4109
1 H D -2.1330
2 H D -2.5070
3 H D -2.4666
4 H D -2.2735
5 H D -2.4886
6 H D -2.1442
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 -6.6337 -5.8623 View CSV PDB
4.5 -6.5782 -5.817 View CSV PDB
5.0 -6.4294 -5.6924 View CSV PDB
5.5 -6.1067 -5.4115 View CSV PDB
6.0 -5.5995 -4.9532 View CSV PDB
6.5 -5.0539 -4.453 View CSV PDB
7.0 -4.6519 -4.0921 View CSV PDB
7.5 -4.4393 -3.9105 View CSV PDB
8.0 -4.3514 -3.8392 View CSV PDB
8.5 -4.3201 -3.8147 View CSV PDB
9.0 -4.3098 -3.8067 View CSV PDB