Project name: f1259a39cd88e22

Status: done

Started: 2025-03-14 20:27:58
Chain sequence(s) A: AGTYGLGD
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:03)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/f1259a39cd88e22/tmp/folded.pdb                (00:00:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:57)
Show buried residues
Minimal score value
-1.6931
Maximal score value
1.3481
Average score
0.0335
Total score value
0.2679
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
15 A A -0.2864
16 G A -0.1608
17 T A 0.4278
18 Y A 1.3481
19 G A 0.2901
20 L A 0.9256
21 G A -0.5834
22 D A -1.6931
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 1.0409 2.5517 View CSV PDB
4.5 0.9825 2.4649 View CSV PDB
5.0 0.9102 2.3574 View CSV PDB
5.5 0.8318 2.2408 View CSV PDB
6.0 0.7513 2.1796 View CSV PDB
6.5 0.6701 2.1796 View CSV PDB
7.0 0.5888 2.1795 View CSV PDB
7.5 0.5082 2.1792 View CSV PDB
8.0 0.4292 2.1782 View CSV PDB
8.5 0.3554 2.1751 View CSV PDB
9.0 0.2932 2.1654 View CSV PDB