Project name: GCG WT

Status: done

Started: 2026-04-23 13:10:57
Chain sequence(s) A: HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
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                                                (00:00:19)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:03:08)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:03:09)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:03:09)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:12)
Show buried residues
Minimal score value
-2.4825
Maximal score value
2.6961
Average score
-0.3404
Total score value
-9.8721
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 H A -1.8061
2 S A -1.2047
3 Q A -1.8737
4 G A -1.1098
5 T A 0.1396
6 F A 1.5414
7 T A 0.2661
8 S A -0.8469
9 D A -1.5786
10 Y A 0.3233
11 S A -0.6327
12 K A -2.3380
13 Y A -0.9564
14 L A -0.4056
15 D A -2.4412
16 S A -2.0852
17 R A -2.4825
18 R A -2.4792
19 A A -1.2080
20 Q A -0.9756
21 D A -0.4507
22 F A 2.0428
23 V A 2.0853
24 Q A 1.0838
25 W A 2.1717
26 L A 2.6961
27 M A 1.8366
28 N A 0.0821
29 T A 0.7340
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, -0.3404 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_9 -0.3404 View CSV PDB
model_0 -0.4053 View CSV PDB
model_1 -0.4676 View CSV PDB
model_10 -0.4887 View CSV PDB
model_11 -0.4942 View CSV PDB
model_4 -0.5294 View CSV PDB
model_6 -0.5354 View CSV PDB
CABS_average -0.5599 View CSV PDB
model_7 -0.6215 View CSV PDB
model_2 -0.6272 View CSV PDB
model_5 -0.7025 View CSV PDB
model_3 -0.7189 View CSV PDB
model_8 -0.788 View CSV PDB
input -0.8139 View CSV PDB