Project name: positive control

Status: done

Started: 2026-03-06 16:55:49
Chain sequence(s) A: ERIEKLREKKKKLKTRLDKLRERYKRIK
B: ERIEKLREKKKKLKTRLDKLRERYKRIK
input PDB
Selected Chain(s) A,B
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 all 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                                          (00:06:30)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d1d9bc141c8ab7c/tmp/folded.pdb                (00:06:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:56)
Show buried residues
Minimal score value
-5.3846
Maximal score value
0.0
Average score
-3.5731
Total score value
-200.0914
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 E A -3.5363
2 R A -3.7236
3 I A -3.5055
4 E A -4.7440
5 K A -4.9621
6 L A 0.0000
7 R A -4.9136
8 E A -4.9036
9 K A -4.3515
10 K A -4.3080
11 K A -4.2149
12 K A -3.4381
13 L A -2.7061
14 K A -3.0926
15 T A -2.5518
16 R A -3.0072
17 L A 0.0000
18 D A -2.9499
19 K A -3.2467
20 L A 0.0000
21 R A -4.2498
22 E A -4.2949
23 R A -3.7634
24 Y A -3.4618
25 K A -4.1925
26 R A -3.7065
27 I A -1.9546
28 K A -2.7081
1 E B -3.5280
2 R B -3.5097
3 I B -2.9160
4 E B -4.3169
5 K B -4.4755
6 L B -3.6173
7 R B -3.9042
8 E B -4.1722
9 K B -3.6653
10 K B -3.8535
11 K B -3.9957
12 K B -3.2976
13 L B -2.9763
14 K B -3.5018
15 T B -2.9017
16 R B -3.2262
17 L B -3.6612
18 D B -3.6206
19 K B -4.1679
20 L B -4.2805
21 R B -5.0275
22 E B -5.3846
23 R B -4.9130
24 Y B -4.3318
25 K B -4.6791
26 R B -4.1578
27 I B -2.5737
28 K B -2.9487
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 -6.3621 0.0 View CSV PDB
4.5 -6.5078 0.0 View CSV PDB
5.0 -6.6844 0.0 View CSV PDB
5.5 -6.8308 0.0 View CSV PDB
6.0 -6.867 0.0 View CSV PDB
6.5 -6.7325 0.0 View CSV PDB
7.0 -6.437 0.0 View CSV PDB
7.5 -6.0419 0.0 View CSV PDB
8.0 -5.602 0.0 View CSV PDB
8.5 -5.1439 0.0 View CSV PDB
9.0 -4.6792 0.0 View CSV PDB