Project name: a2510483ed7b44d

Status: done

Started: 2025-03-29 11:41:36
Chain sequence(s) A: AATFDE
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                                          (00:00:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a2510483ed7b44d/tmp/folded.pdb                (00:00:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:26)
Show buried residues
Minimal score value
-2.2619
Maximal score value
0.6616
Average score
-0.4279
Total score value
-2.5672
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 A A 0.2928
2 A A 0.3501
3 T A 0.2015
4 F A 0.6616
5 D A -1.8113
6 E A -2.2619
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 2.1658 4.425 View CSV PDB
4.5 1.9712 4.2254 View CSV PDB
5.0 1.706 3.9579 View CSV PDB
5.5 1.4065 3.6579 View CSV PDB
6.0 1.1033 3.353 View CSV PDB
6.5 0.8217 3.0641 View CSV PDB
7.0 0.5806 2.8065 View CSV PDB
7.5 0.3783 2.5793 View CSV PDB
8.0 0.2005 2.3726 View CSV PDB
8.5 0.0415 2.1848 View CSV PDB
9.0 -0.0893 2.0294 View CSV PDB