Project name: 003

Status: done

Started: 2026-10-21 11:34:17
Settings
Chain sequence(s) MLDLINTSLKEQRRLLDEESERNEELKKNKTDIARHGEDVMQFFKDRLGK input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[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                                          (00:01:11)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/f7ef4c7caffabb/tmp/folded.pdb                 (00:01:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:33)
Show buried residues
Minimal score value
-5.8747
Maximal score value
1.7832
Average score
-2.3652
Total score value
-118.2624
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 M A 1.7832
2 L A 1.6317
3 D A -0.0692
4 L A 1.4242
5 I A 1.0243
6 N A -0.7916
7 T A -0.8528
8 S A -1.0274
9 L A -1.4125
10 K A -2.8189
11 E A -2.8616
12 Q A -2.6797
13 R A -3.5934
14 R A -3.4647
15 L A -2.0672
16 L A -2.1242
17 D A -4.1358
18 E A -4.7606
19 E A -4.6681
20 S A -4.1966
21 E A -5.5463
22 R A -5.8115
23 N A -5.2139
24 E A -5.8747
25 E A -5.5626
26 L A -4.1326
27 K A -4.8168
28 K A -4.4940
29 N A -3.2574
30 K A -3.2996
31 T A -2.5063
32 D A -2.1812
33 I A -0.8276
34 A A -1.7347
35 R A -3.0510
36 H A -2.4022
37 G A -1.5113
38 E A -2.6807
39 D A -2.3221
40 V A -0.0249
41 M A -0.2317
42 Q A -1.5484
43 F A 0.4199
44 F A -0.2872
45 K A -2.4529
46 D A -2.7885
47 R A -2.3964
48 L A -1.1367
49 G A -2.1840
50 K A -2.7442
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.

pH
Average A3D Score
Max A3D Score
4.0 -2.373 3.572 View CSV PDB
4.5 -2.6408 3.3438 View CSV PDB
5.0 -2.9759 3.0626 View CSV PDB
5.5 -3.3135 2.7702 View CSV PDB
6.0 -3.5832 2.5034 View CSV PDB
6.5 -3.7376 2.2832 View CSV PDB
7.0 -3.7775 2.1282 View CSV PDB
7.5 -3.7403 2.0011 View CSV PDB
8.0 -3.6612 1.8896 View CSV PDB
8.5 -3.5525 1.8087 View CSV PDB
9.0 -3.4111 1.7648 View CSV PDB