Project name: case_study_7ZSS

Status: done

Started: 2026-04-08 06:35:12
Chain sequence(s) D: TNMLEALQQRLQFYHGQVARAALENNSGKARRFGRIVKQYEDAIKLYKAGKPVPYDELPVPPGFG
input PDB
Selected Chain(s) D
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
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 D chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:21)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:08:04)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:08:04)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:08:04)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:08:05)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:08:06)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:08:06)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:08:06)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:08:06)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:08:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:10)
Show buried residues
Minimal score value
-3.5984
Maximal score value
0.9722
Average score
-1.2165
Total score value
-79.0743
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 T D -0.6416
2 N D -1.5759
3 M D -0.2818
4 L D -1.0498
5 E D -2.4885
6 A D -1.7062
7 L D 0.0000
8 Q D -2.3449
9 Q D -2.0567
10 R D -1.4473
11 L D -1.2699
12 Q D -1.3146
13 F D 0.3685
14 Y D 0.0000
15 H D -1.3842
16 G D -0.7538
17 Q D -0.8618
18 V D -1.4223
19 A D -0.8587
20 R D -2.2162
21 A D 0.0000
22 A D -1.4157
23 L D -0.5266
24 E D -2.6000
25 N D -2.7398
26 N D -2.9929
27 S D -2.4223
28 G D -2.5646
29 K D -3.0788
30 A D -2.8135
31 R D -3.5984
32 R D -3.4945
33 F D 0.0000
34 G D -2.4833
35 R D -2.9652
36 I D 0.0000
37 V D -2.0030
38 K D -2.9635
39 Q D -1.9434
40 Y D 0.0000
41 E D -2.1587
42 D D -1.8065
43 A D 0.0000
44 I D -1.4495
45 K D -2.1524
46 L D -0.8227
47 Y D -0.8083
48 K D -1.9856
49 A D -1.2709
50 G D -1.2968
51 K D -1.3421
52 P D -0.4996
53 V D 0.0000
54 P D -0.1937
55 Y D 0.5923
56 D D -0.8328
57 E D -0.1525
58 L D 0.9722
59 P D -0.1166
60 V D 0.0000
61 P D -0.0002
62 P D -0.2608
63 G D 0.1516
64 F D 0.3120
65 G D -0.0415
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -1.2165 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_10 -1.2165 View CSV PDB
model_4 -1.35 View CSV PDB
input -1.3555 View CSV PDB
model_11 -1.4273 View CSV PDB
model_8 -1.4329 View CSV PDB
model_7 -1.4345 View CSV PDB
CABS_average -1.4747 View CSV PDB
model_3 -1.4774 View CSV PDB
model_0 -1.4902 View CSV PDB
model_1 -1.5135 View CSV PDB
model_5 -1.5359 View CSV PDB
model_6 -1.5661 View CSV PDB
model_9 -1.5867 View CSV PDB
model_2 -1.6658 View CSV PDB