Project name: peptide_14

Status: done

Started: 2026-05-02 11:02:25
Chain sequence(s) A: LRARASGSARIYQAGRDQHITER
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]                                                (00:00:00)
[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                                                (00:00:18)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:19)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:21)
Show buried residues
Minimal score value
-2.9969
Maximal score value
1.4556
Average score
-1.0643
Total score value
-24.4792
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 L A 0.0153
2 R A -1.9592
3 A A -1.5330
4 R A -2.5332
5 A A -1.6420
6 S A -1.0704
7 G A -0.8582
8 S A -0.1958
9 A A 0.0000
10 R A -1.3117
11 I A 1.4556
12 Y A 0.8867
13 Q A -0.6209
14 A A -0.1105
15 G A -0.5188
16 R A -1.4169
17 D A -1.1762
18 Q A -2.2543
19 H A -2.0604
20 I A -0.1755
21 T A -1.6233
22 E A -2.9969
23 R A -2.7796
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, -1.0643 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_4 -1.0643 View CSV PDB
model_1 -1.1639 View CSV PDB
model_5 -1.3106 View CSV PDB
model_10 -1.392 View CSV PDB
model_7 -1.4144 View CSV PDB
model_11 -1.4312 View CSV PDB
CABS_average -1.4754 View CSV PDB
input -1.4954 View CSV PDB
model_2 -1.5652 View CSV PDB
model_3 -1.6132 View CSV PDB
model_9 -1.6225 View CSV PDB
model_8 -1.6972 View CSV PDB
model_0 -1.7053 View CSV PDB
model_6 -1.725 View CSV PDB