Project name: PSMa1

Status: done

Started: 2026-03-29 13:09:34
Chain sequence(s) A: MGIIAGIIKVIKSLIEQFTGT
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:17)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:01:55)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:01:56)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:01:56)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:01:56)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:57)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:57)
Show buried residues
Minimal score value
-1.3192
Maximal score value
2.3487
Average score
0.7036
Total score value
14.7751
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 0.9653
2 G A 0.1151
3 I A 2.2588
4 I A 2.1523
5 A A 0.3336
6 G A -0.1212
7 I A 2.2680
8 I A 1.7553
9 K A -1.0777
10 V A 1.8290
11 I A 2.3487
12 K A -0.3702
13 S A -0.1664
14 L A 1.8785
15 I A 1.4279
16 E A -1.3192
17 Q A -0.9464
18 F A 1.7014
19 T A 0.2519
20 G A -0.3930
21 T A -0.1166
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, 0.7036 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 0.7036 View CSV PDB
model_11 0.6874 View CSV PDB
model_4 0.6307 View CSV PDB
model_10 0.618 View CSV PDB
model_0 0.5682 View CSV PDB
model_6 0.5639 View CSV PDB
CABS_average 0.5559 View CSV PDB
model_8 0.5341 View CSV PDB
model_7 0.5192 View CSV PDB
model_2 0.5012 View CSV PDB
model_3 0.4994 View CSV PDB
input 0.4639 View CSV PDB
model_5 0.4451 View CSV PDB
model_9 0.4001 View CSV PDB