Project name: miniprotein1-dynamic

Status: done

Started: 2026-04-26 16:32:13
Chain sequence(s) A: RVRQYRNPHTGEVIETRGGNHRTYREWKARWGPEAVESWATLL
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:21)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:09:48)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:09:49)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:09:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:54)
Show buried residues
Minimal score value
-3.6115
Maximal score value
1.2754
Average score
-1.4211
Total score value
-61.1064
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 R A -1.7136
2 V A -1.1667
3 R A -1.1510
4 Q A -0.9748
5 Y A 0.0000
6 R A -2.4376
7 N A 0.0000
8 P A -1.5182
9 H A -1.7213
10 T A -1.4679
11 G A -1.7988
12 E A -1.9358
13 V A -0.7227
14 I A -1.0072
15 E A -1.8712
16 T A 0.0000
17 R A -2.8426
18 G A -2.7249
19 G A -2.5935
20 N A -2.8472
21 H A -3.0783
22 R A -3.2130
23 T A -2.2331
24 Y A 0.0000
25 R A -3.6115
26 E A -2.4949
27 W A 0.0000
28 K A -2.4145
29 A A -1.6489
30 R A -2.1541
31 W A -1.1084
32 G A -1.5623
33 P A -2.0027
34 E A -2.1941
35 A A -1.3637
36 V A 0.0000
37 E A -1.7381
38 S A -1.1735
39 W A -0.9772
40 A A -0.3544
41 T A 0.2554
42 L A 1.1805
43 L A 1.2754
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, -1.4211 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
input -1.4211 View CSV PDB
model_0 -1.4554 View CSV PDB
model_5 -1.4775 View CSV PDB
model_8 -1.4927 View CSV PDB
model_2 -1.5301 View CSV PDB
model_4 -1.5355 View CSV PDB
model_3 -1.5968 View CSV PDB
CABS_average -1.6057 View CSV PDB
model_11 -1.6082 View CSV PDB
model_9 -1.6807 View CSV PDB
model_10 -1.6946 View CSV PDB
model_6 -1.7176 View CSV PDB
model_7 -1.7248 View CSV PDB
model_1 -1.7542 View CSV PDB