Project name: AB06-PrD

Status: done

Started: 2025-04-25 15:47:14
Chain sequence(s) A: QQQQQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQPQPPPPPPPPPPGP
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                                          (00:00:25)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/3e2caf4cfab750/tmp/folded.pdb                 (00:00:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:43)
Show buried residues
Minimal score value
-4.9094
Maximal score value
1.591
Average score
-1.9857
Total score value
-121.1296
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 -3.0089
2 Q A -3.6019
3 Q A -4.0758
4 Q A -4.4586
5 Q A -4.7437
6 Q A -4.9094
7 Q A -4.8681
8 Q A -4.8239
9 Q A -4.9026
10 Q A -4.8735
11 Q A -4.8492
12 Q A -4.7566
13 Q A -4.5956
14 Q A -4.6673
15 Q A -4.5835
16 Q A -4.3823
17 Q A -4.4940
18 Q A -4.3177
19 Q A -3.8485
20 Q A -3.5638
21 Q A -3.1013
22 P A -1.7109
23 P A -1.1820
24 P A -0.8327
25 P A -0.6988
26 P A -0.6963
27 P A -0.6952
28 P A -0.6972
29 P A -0.6964
30 P A -0.8383
31 P A -0.6904
32 P A -0.6823
33 Q A -0.9196
34 L A 0.3838
35 P A -0.5307
36 Q A -1.3201
37 P A -1.0708
38 P A -1.1585
39 P A -1.3654
40 Q A -1.7804
41 A A -1.0337
42 Q A -1.0067
43 P A 0.1641
44 L A 1.5910
45 L A 1.5558
46 P A 0.0416
47 Q A -1.1216
48 P A -1.3608
49 Q A -1.9019
50 P A -1.2810
51 P A -0.9345
52 P A -0.8280
53 P A -0.6941
54 P A -0.6953
55 P A -0.6941
56 P A -0.6941
57 P A -0.7306
58 P A -0.7505
59 P A -0.7612
60 G A -0.8168
61 P A -0.5688
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 1.1289 4.872 View CSV PDB
4.5 1.1289 4.872 View CSV PDB
5.0 1.1289 4.872 View CSV PDB
5.5 1.1289 4.872 View CSV PDB
6.0 1.1289 4.872 View CSV PDB
6.5 1.1289 4.872 View CSV PDB
7.0 1.1289 4.872 View CSV PDB
7.5 1.1289 4.872 View CSV PDB
8.0 1.1289 4.872 View CSV PDB
8.5 1.1289 4.872 View CSV PDB
9.0 1.1289 4.872 View CSV PDB