Project name: PDE8B_shortest_dynamic

Status: done

Started: 2026-07-29 13:36:49
Chain sequence(s) A: MGCAPSIHVSQSGVIYCRDSDESSSP
input PDB
Selected Chain(s) A
Distance of aggregation 5 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 A 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                                                (00:00:07)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:26)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:28)
Show buried residues
Minimal score value
-2.1575
Maximal score value
2.7953
Average score
0.0541
Total score value
1.4058
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 M A 0.9669
2 G A -0.1354
3 C A 0.6560
4 A A 0.1150
5 P A -0.2451
6 S A 0.1807
7 I A 1.4016
8 H A 0.0686
9 V A 1.9392
10 S A 0.0158
11 Q A -1.2541
12 S A -0.5199
13 G A -0.1751
14 V A 2.0618
15 I A 2.7953
16 Y A 1.5453
17 C A 0.9451
18 R A -0.9754
19 D A -1.9404
20 S A -0.6676
21 D A -1.9625
22 E A -2.1575
23 S A -0.5577
24 S A -0.1327
25 S A -0.2688
26 P A -0.2933
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, 0.0541 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
input 0.0541 View CSV PDB
model_6 0.0536 View CSV PDB
model_1 0.027 View CSV PDB
model_11 0.0206 View CSV PDB
model_3 0.0193 View CSV PDB
model_0 0.0172 View CSV PDB
model_2 0.0048 View CSV PDB
CABS_average -0.0317 View CSV PDB
model_4 -0.0616 View CSV PDB
model_9 -0.0704 View CSV PDB
model_7 -0.0754 View CSV PDB
model_8 -0.078 View CSV PDB
model_5 -0.0817 View CSV PDB
model_10 -0.1562 View CSV PDB