Project name: 63febba3105208d

Status: done

Started: 2024-04-29 02:51:54
Chain sequence(s) A: MGSWAEFKQRLAAIKTRLQALGGSEAELAAFEKEIAAFESELQAYKGKGNPEVEALRKEAAAIRDELQAYRHN
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                                                (00:01:00)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:07:20)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:07:20)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:07:20)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:07:21)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:07:21)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:07:21)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:07:22)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:07:22)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:07:22)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:07:22)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:07:22)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:07:23)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:07:23)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:07:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:07:25)
Show buried residues
Minimal score value
-4.0233
Maximal score value
0.6404
Average score
-1.7448
Total score value
-127.3706
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 M A 0.6404
2 G A -0.1309
3 S A -0.5965
4 W A -0.7098
5 A A -1.2493
6 E A -2.4659
7 F A -2.1979
8 K A -3.0384
9 Q A -3.2739
10 R A -3.3281
11 L A 0.0000
12 A A -2.1718
13 A A -1.9226
14 I A 0.0000
15 K A -2.4481
16 T A -1.5888
17 R A -2.2278
18 L A 0.0000
19 Q A -2.0718
20 A A -1.1732
21 L A -1.2655
22 G A -1.3794
23 G A -1.9790
24 S A -1.6519
25 E A -2.6813
26 A A -1.4150
27 E A -1.8472
28 L A 0.0000
29 A A -1.6132
30 A A -1.3791
31 F A 0.0000
32 E A -1.9210
33 K A -2.2215
34 E A -1.8560
35 I A 0.0000
36 A A -1.2511
37 A A -1.2134
38 F A 0.0000
39 E A -1.9796
40 S A -1.4597
41 E A -1.4499
42 L A 0.0000
43 Q A -2.9792
44 A A -2.0902
45 Y A 0.0000
46 K A -4.0233
47 G A -2.6865
48 K A -3.1152
49 G A -2.7792
50 N A -2.1098
51 P A -2.0458
52 E A -3.3734
53 V A 0.0000
54 E A -4.0151
55 A A -2.8365
56 L A 0.0000
57 R A -3.7660
58 K A -3.4359
59 E A -2.7611
60 A A 0.0000
61 A A -2.1166
62 A A -1.9235
63 I A 0.0000
64 R A -2.3930
65 D A -2.7879
66 E A -2.5018
67 L A 0.0000
68 Q A -2.7671
69 A A -2.0528
70 Y A -2.1712
71 R A -2.8209
72 H A -2.8709
73 N A -2.4295
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, -1.7448 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_3 -1.7448 View CSV PDB
model_4 -1.7464 View CSV PDB
model_6 -1.7553 View CSV PDB
model_1 -1.7979 View CSV PDB
model_10 -1.8273 View CSV PDB
CABS_average -1.8308 View CSV PDB
model_0 -1.8345 View CSV PDB
model_9 -1.8378 View CSV PDB
model_5 -1.8614 View CSV PDB
model_7 -1.8658 View CSV PDB
model_11 -1.877 View CSV PDB
model_2 -1.9106 View CSV PDB
model_8 -1.9114 View CSV PDB
input -2.0785 View CSV PDB