Project name: PhoxHD

Status: done

Started: 2026-06-05 09:36:07
Chain sequence(s) A: ASQRRIRTTFTSAQLKELERVFAETHYPDIYTREELALKIDLTEARVQVWFQNRRAKFRKQER
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                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:15)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:07:24)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:07:24)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:07:25)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:07:25)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:07:25)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:07:25)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:07:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:07:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:07:26)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:07:26)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:07:26)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:07:26)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:07:27)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:07:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:29)
Show buried residues
Minimal score value
-3.4992
Maximal score value
1.3934
Average score
-1.1964
Total score value
-75.3762
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 A A -0.8995
2 S A -1.2003
3 Q A -1.9967
4 R A -2.4555
5 R A 0.0000
6 I A 0.0000
7 R A -2.0565
8 T A -1.2977
9 T A -0.6866
10 F A -0.5269
11 T A -0.6894
12 S A -0.7837
13 A A -0.8662
14 Q A 0.0000
15 L A -1.6640
16 K A -2.7900
17 E A -2.4057
18 L A 0.0000
19 E A -2.9047
20 R A -3.2615
21 V A -2.3030
22 F A 0.0000
23 A A -1.8953
24 E A -1.7221
25 T A -1.5110
26 H A -1.6744
27 Y A 0.0000
28 P A -0.5011
29 D A -0.2092
30 I A 1.3934
31 Y A 1.3384
32 T A -0.1452
33 R A -0.4954
34 E A -0.7712
35 E A -0.9019
36 L A 0.0000
37 A A 0.0000
38 L A -0.4792
39 K A -1.5185
40 I A -1.0290
41 D A -1.9111
42 L A 0.0000
43 T A -1.6434
44 E A -1.6725
45 A A -1.1934
46 R A -1.9791
47 V A 0.0000
48 Q A -0.8474
49 V A -0.0550
50 W A 0.0000
51 F A -0.7683
52 Q A -1.6332
53 N A -1.4030
54 R A 0.0000
55 R A -2.1924
56 A A -2.1355
57 K A -2.3358
58 F A -1.6254
59 R A -2.9795
60 K A -3.4992
61 Q A -2.9522
62 E A -2.9898
63 R A -2.6504
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, -1.1964 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_5 -1.1964 View CSV PDB
model_6 -1.3072 View CSV PDB
model_8 -1.3188 View CSV PDB
model_9 -1.36 View CSV PDB
model_11 -1.3782 View CSV PDB
model_4 -1.4066 View CSV PDB
input -1.4421 View CSV PDB
CABS_average -1.4445 View CSV PDB
model_0 -1.4667 View CSV PDB
model_1 -1.5046 View CSV PDB
model_3 -1.5139 View CSV PDB
model_2 -1.5858 View CSV PDB
model_10 -1.6309 View CSV PDB
model_7 -1.6654 View CSV PDB