Project name: rockt

Status: done

Started: 2026-03-10 11:21:37
Chain sequence(s) A: KWKIFKKIERLGQNIRDGIIKAGPAVAVVGQA
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage No
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]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:02:34)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:02:34)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:35)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:37)
Show buried residues
Minimal score value
-1.9387
Maximal score value
2.1878
Average score
-0.0685
Total score value
-2.1915
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 K A -1.4758
2 W A 0.5422
3 K A -1.0960
4 I A 1.7773
5 F A 1.4533
6 K A -1.9387
7 K A -1.4967
8 I A 1.0288
9 E A -1.8699
10 R A -1.8782
11 L A 1.0019
12 G A -0.2774
13 Q A -1.5498
14 N A -0.6671
15 I A 0.0896
16 R A -1.8011
17 D A -0.9267
18 G A 0.0000
19 I A 2.1878
20 I A 1.9416
21 K A -1.1758
22 A A -0.2662
23 G A -0.1522
24 P A -0.2743
25 A A 0.3790
26 V A 1.5059
27 A A 0.5736
28 V A 1.9683
29 V A 2.0650
30 G A -0.3642
31 Q A -1.2756
32 A A -0.2201
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, -0.0685 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_6 -0.0685 View CSV PDB
input -0.0732 View CSV PDB
model_3 -0.0953 View CSV PDB
model_10 -0.108 View CSV PDB
model_7 -0.1317 View CSV PDB
model_11 -0.1544 View CSV PDB
model_2 -0.162 View CSV PDB
model_4 -0.1745 View CSV PDB
CABS_average -0.183 View CSV PDB
model_8 -0.2183 View CSV PDB
model_9 -0.2481 View CSV PDB
model_0 -0.2652 View CSV PDB
model_1 -0.2667 View CSV PDB
model_5 -0.3033 View CSV PDB