Project name: N_half_ml

Status: done

Started: 2025-10-03 10:14:30
Chain sequence(s) A: KKKLVIIYGKKGSGKTKKYEKEKKKAKKTPNAKVVIVSTEEELKKEKEKAKELGIEVK
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                                          (00:03:08)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2fdfe4bb9cc21ee/tmp/folded.pdb                (00:03:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:33)
Show buried residues
Minimal score value
-5.2908
Maximal score value
0.5665
Average score
-2.8388
Total score value
-164.6533
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 K A -3.6603
2 K A -3.6706
3 K A -3.2744
4 L A 0.0000
5 V A -0.9043
6 I A 0.1196
7 I A 0.0000
8 Y A 0.0126
9 G A -1.2693
10 K A -2.8569
11 K A -2.8940
12 G A -2.0764
13 S A -1.9276
14 G A -2.0954
15 K A -2.2051
16 T A -2.4459
17 K A -3.7486
18 K A -3.5104
19 Y A -3.0838
20 E A -4.5915
21 K A -4.6512
22 E A -4.2102
23 K A -4.8019
24 K A -4.8246
25 K A -4.7160
26 A A -4.2439
27 K A -4.3635
28 K A -3.7070
29 T A -2.7542
30 P A -2.3930
31 N A -3.4291
32 A A -3.5963
33 K A -3.3461
34 V A 0.0000
35 V A 0.2405
36 I A 0.5665
37 V A 0.0000
38 S A -1.6720
39 T A -2.5833
40 E A -3.7497
41 E A -4.1901
42 E A -3.7320
43 L A -3.1731
44 K A -4.9528
45 K A -5.0817
46 E A -4.2648
47 K A -4.3300
48 E A -5.2908
49 K A -4.6814
50 A A 0.0000
51 K A -4.1353
52 E A -3.5611
53 L A -2.2128
54 G A -2.4935
55 I A -3.0970
56 E A -3.0705
57 V A -2.0756
58 K A -1.9935
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 -4.228 0.5185 View CSV PDB
4.5 -4.352 0.4947 View CSV PDB
5.0 -4.4962 0.4645 View CSV PDB
5.5 -4.5902 0.4405 View CSV PDB
6.0 -4.5452 0.4408 View CSV PDB
6.5 -4.3048 0.4809 View CSV PDB
7.0 -3.8916 0.5595 View CSV PDB
7.5 -3.3759 0.6619 View CSV PDB
8.0 -2.8162 0.7747 View CSV PDB
8.5 -2.2426 0.8908 View CSV PDB
9.0 -1.6711 1.0706 View CSV PDB