Project name: miniprotein2-dynamic

Status: done

Started: 2026-04-27 00:51:27
Chain sequence(s) A: WEKAEKALKEHPELYKEKEIKPPKVTWKFPPETITIEGKEAEEYAKRN
input PDB
Selected Chain(s) A
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 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                                                (00:00:54)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:06:09)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:06:09)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:06:09)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:06:09)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:06:10)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:06:10)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:06:10)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:06:10)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:06:10)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:06:11)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:06:11)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:06:11)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:06:11)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:06:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:15)
Show buried residues
Minimal score value
-3.5258
Maximal score value
1.433
Average score
-1.3431
Total score value
-64.4679
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 W A -0.3393
2 E A -2.4711
3 K A -2.6855
4 A A -2.7276
5 E A -3.2026
6 K A -3.2131
7 A A -2.2799
8 L A -1.0281
9 K A -2.4470
10 E A -2.6060
11 H A -1.3598
12 P A -1.3879
13 E A -1.9690
14 L A -0.1430
15 Y A -0.5942
16 K A -2.4196
17 E A -1.6887
18 K A -1.6910
19 E A -2.1162
20 I A -0.0923
21 K A -0.7188
22 P A -1.3591
23 P A -0.9011
24 K A 0.0000
25 V A 1.1098
26 T A 0.2892
27 W A 0.0000
28 K A -0.3909
29 F A 0.7692
30 P A -0.1613
31 P A -0.0771
32 E A -1.3748
33 T A 0.1673
34 I A 1.4330
35 T A 0.9822
36 I A 0.8280
37 E A -1.0720
38 G A -1.9305
39 K A -2.7605
40 E A 0.0000
41 A A -2.0187
42 E A -3.4555
43 E A -3.0866
44 Y A -2.1060
45 A A -2.5974
46 K A -3.5258
47 R A -3.4538
48 N A -2.5948
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, -1.3431 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_1 -1.3431 View CSV PDB
model_7 -1.3994 View CSV PDB
model_9 -1.4805 View CSV PDB
model_2 -1.5257 View CSV PDB
model_8 -1.5697 View CSV PDB
CABS_average -1.641 View CSV PDB
model_3 -1.6532 View CSV PDB
model_4 -1.6904 View CSV PDB
model_0 -1.6925 View CSV PDB
model_5 -1.7398 View CSV PDB
model_11 -1.7686 View CSV PDB
input -1.7906 View CSV PDB
model_6 -1.8167 View CSV PDB
model_10 -2.0117 View CSV PDB