Project name: 53bf5ee1d85e543

Status: done

Started: 2025-03-18 10:03:23
Chain sequence(s) A: GDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLK
input PDB
Selected Chain(s) A
Distance of aggregation 5 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                                                (00:01:05)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:07:17)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:07:17)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:07:17)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:07:18)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:07:18)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:07:18)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:07:18)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:07:18)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:07:19)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:07:19)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:07:19)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:07:19)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:07:19)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:07:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:21)
Show buried residues
Minimal score value
-2.4407
Maximal score value
1.7049
Average score
-0.4039
Total score value
-26.2545
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 G A -0.5074
2 D A -0.3110
3 P A -0.0340
4 I A 0.1981
5 P A -0.4353
6 K A -1.6660
7 V A -0.0386
8 E A -0.9298
9 F A 1.7049
10 T A -0.0728
11 E A -2.1724
12 E A -2.4407
13 E A -0.9097
14 I A 0.0000
15 K A -1.8447
16 T A -0.3660
17 W A 0.3181
18 G A 0.0000
19 T A 0.1446
20 V A 0.7648
21 F A 0.0000
22 Q A -0.9914
23 E A -1.8681
24 L A 0.2974
25 N A -0.9058
26 K A -1.7302
27 L A 1.2760
28 Y A 0.4796
29 P A -0.2219
30 T A -0.3073
31 H A -0.9924
32 A A -0.0907
33 C A -0.1265
34 R A -2.1201
35 E A -2.0140
36 Y A 0.5133
37 L A -0.1299
38 K A -1.7101
39 N A -0.5732
40 L A 0.0000
41 P A -0.0898
42 L A 0.2934
43 L A 0.0000
44 S A -0.4346
45 K A -1.5535
46 Y A 0.5569
47 C A 0.3125
48 G A -0.0270
49 Y A 1.1970
50 R A -0.1871
51 E A -0.9758
52 D A -1.7417
53 N A -1.0625
54 I A 0.1014
55 P A 0.0000
56 Q A -0.9303
57 L A 0.9812
58 E A -1.6104
59 D A -0.8543
60 V A 0.0781
61 S A -0.4430
62 N A -1.1456
63 F A 1.0961
64 L A 1.4026
65 K A -1.4049
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, -0.4039 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_7 -0.4039 View CSV PDB
model_6 -0.4284 View CSV PDB
model_11 -0.4395 View CSV PDB
model_0 -0.4576 View CSV PDB
model_1 -0.4739 View CSV PDB
CABS_average -0.4786 View CSV PDB
model_4 -0.4805 View CSV PDB
model_3 -0.4839 View CSV PDB
model_9 -0.4842 View CSV PDB
input -0.4929 View CSV PDB
model_10 -0.4964 View CSV PDB
model_5 -0.5267 View CSV PDB
model_8 -0.5272 View CSV PDB
model_2 -0.541 View CSV PDB