Project name: 23e

Status: done

Started: 2026-05-10 13:10:30
Chain sequence(s) A: AAAADVDIINELSAKYNLNHTQKLGVLSALTSGVEKATKLIAGYAKFDIIDAATAAEMMTGVNLAAAHLA
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 globular. Max 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                                          (00:00:49)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/bc16054d0168c5b/tmp/folded.pdb                (00:00:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:17)
Show buried residues
Minimal score value
-3.1455
Maximal score value
1.4148
Average score
-0.5862
Total score value
-41.0363
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 0.0967
2 A A 0.2417
3 A A 0.1835
4 A A -0.1875
5 D A -0.1533
6 V A 0.3115
7 D A -1.8360
8 I A -1.0276
9 I A 0.0000
10 N A -2.7350
11 E A -3.1455
12 L A 0.0000
13 S A -2.2992
14 A A -1.8788
15 K A -2.3210
16 Y A -0.9585
17 N A -2.0370
18 L A -1.6739
19 N A -1.6840
20 H A -1.6870
21 T A -0.7975
22 Q A -0.9872
23 K A -1.1410
24 L A 0.1340
25 G A 0.0000
26 V A 0.0000
27 L A 0.8269
28 S A 0.1066
29 A A 0.0000
30 L A 0.7821
31 T A -0.0256
32 S A -0.5722
33 G A -0.7390
34 V A -1.1501
35 E A -2.5699
36 K A -2.4733
37 A A 0.0000
38 T A -1.6220
39 K A -2.2053
40 L A -0.9165
41 I A 0.0000
42 A A -0.6539
43 G A -0.1379
44 Y A 0.5934
45 A A -0.4809
46 K A -0.9009
47 F A 0.8799
48 D A -0.5896
49 I A 1.4148
50 I A 0.1276
51 D A -1.4984
52 A A -0.9387
53 A A -0.4797
54 T A -0.2912
55 A A -0.1877
56 A A -0.2839
57 E A -0.6020
58 M A -0.2990
59 M A -0.1240
60 T A -0.4964
61 G A 0.0000
62 V A 0.0000
63 N A -0.9392
64 L A -0.2649
65 A A 0.0000
66 A A 0.0502
67 A A -0.0660
68 H A -0.1853
69 L A 0.9600
70 A A 0.4983
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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.0646 4.1192 View CSV PDB
4.5 -0.1591 3.8778 View CSV PDB
5.0 -0.2649 3.5985 View CSV PDB
5.5 -0.3614 3.3089 View CSV PDB
6.0 -0.4327 3.03 View CSV PDB
6.5 -0.4702 2.8434 View CSV PDB
7.0 -0.476 2.7818 View CSV PDB
7.5 -0.4595 2.7558 View CSV PDB
8.0 -0.4275 2.7561 View CSV PDB
8.5 -0.3811 2.7873 View CSV PDB
9.0 -0.3195 2.8606 View CSV PDB