Project name: AB01-PrD

Status: done

Started: 2025-04-25 15:45:22
Chain sequence(s) A: QQQQQQQQQQQQPPPPAPPAAPQQPLGPSLQPQPPQLQQQQQQQQQQQQQQPPHPLSQLAQLQSQP
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                                          (00:00:44)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/387a4944d967b7/tmp/folded.pdb                 (00:00:44)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:03)
Show buried residues
Minimal score value
-4.1485
Maximal score value
0.8529
Average score
-1.796
Total score value
-118.5336
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 Q A -2.8874
2 Q A -3.3514
3 Q A -3.7932
4 Q A -4.1485
5 Q A -4.1470
6 Q A -3.9209
7 Q A -3.8183
8 Q A -3.8245
9 Q A -3.6692
10 Q A -3.2367
11 Q A -2.8885
12 Q A -2.5902
13 P A -1.4610
14 P A -0.9395
15 P A -0.7513
16 P A -0.5421
17 A A -0.3520
18 P A -0.4200
19 P A -0.3871
20 A A -0.3499
21 A A -0.6233
22 P A -1.2204
23 Q A -1.7244
24 Q A -1.6028
25 P A -0.4896
26 L A 0.6449
27 G A 0.1776
28 P A 0.0006
29 S A 0.0837
30 L A 0.4496
31 Q A -1.0052
32 P A -1.0970
33 Q A -1.6294
34 P A -1.2988
35 P A -1.4900
36 Q A -1.8768
37 L A -1.0317
38 Q A -2.6781
39 Q A -3.0575
40 Q A -3.3093
41 Q A -3.5462
42 Q A -3.5936
43 Q A -3.8352
44 Q A -3.5096
45 Q A -3.4722
46 Q A -3.3049
47 Q A -3.4219
48 Q A -3.3949
49 Q A -3.2674
50 Q A -3.4560
51 Q A -3.0011
52 P A -1.8947
53 P A -1.3656
54 H A -1.4051
55 P A -0.4417
56 L A 0.8529
57 S A -0.1080
58 Q A -0.7279
59 L A 0.6294
60 A A -0.1091
61 Q A -0.9509
62 L A 0.1261
63 Q A -1.2193
64 S A -1.1886
65 Q A -1.6262
66 P A -1.0453
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 -0.0063 4.3151 View CSV PDB
4.5 -0.0061 4.3151 View CSV PDB
5.0 -0.0054 4.3151 View CSV PDB
5.5 -0.0034 4.3151 View CSV PDB
6.0 0.0016 4.3151 View CSV PDB
6.5 0.0112 4.3151 View CSV PDB
7.0 0.0235 4.3151 View CSV PDB
7.5 0.0334 4.3151 View CSV PDB
8.0 0.0387 4.3151 View CSV PDB
8.5 0.0407 4.3151 View CSV PDB
9.0 0.0415 4.3151 View CSV PDB