Project name: SARS-CoV-2 E protein

Status: done

Started: 2026-02-24 07:49:06
Chain sequence(s) X: MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV
input PDB
Selected Chain(s) X
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]                                                (00:00:01)
[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 X 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                                                (00:00:47)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:10:47)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:10:47)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:10:48)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:10:48)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:10:48)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:10:48)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:10:48)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:10:49)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:10:49)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:10:49)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:10:49)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:10:50)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:10:50)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:10:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:54)
Show buried residues
Minimal score value
-2.0395
Maximal score value
6.2788
Average score
1.9411
Total score value
145.5834
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 X 1.9005
2 Y X 2.4352
3 S X 2.1171
4 F X 2.5734
5 V X 1.9899
6 S X -0.3082
7 E X -2.0395
8 E X -1.8564
9 T X -1.1745
10 G X -0.6353
11 T X 0.3615
12 L X 2.1727
13 I X 3.0134
14 V X 2.1885
15 N X 1.2729
16 S X 2.6695
17 V X 4.2083
18 L X 3.9772
19 L X 4.0536
20 F X 5.5396
21 L X 5.3716
22 A X 4.8528
23 F X 6.2788
24 V X 6.0819
25 V X 5.8748
26 F X 6.0293
27 L X 4.9356
28 L X 4.9313
29 V X 4.5950
30 T X 3.4647
31 L X 3.0287
32 A X 2.8375
33 I X 3.0907
34 L X 2.0663
35 T X 0.9534
36 A X 1.2001
37 L X 1.5193
38 R X -0.2090
39 L X 1.2581
40 C X 1.2988
41 A X 0.8497
42 Y X 1.8549
43 C X 1.7016
44 C X 1.7895
45 N X 0.8788
46 I X 3.0355
47 V X 2.6916
48 N X 0.9621
49 V X 2.7724
50 S X 1.7745
51 L X 2.4757
52 V X 1.9800
53 K X 0.0642
54 P X 1.1343
55 S X 2.5179
56 F X 3.3877
57 Y X 3.3137
58 V X 3.6710
59 Y X 2.8298
60 S X 1.3728
61 R X 0.5342
62 V X 1.2932
63 K X -1.1050
64 N X -1.7714
65 L X -0.2172
66 N X -1.5593
67 S X -1.0852
68 S X -1.1564
69 R X -1.6324
70 V X 0.3848
71 P X -0.1673
72 D X -0.3434
73 L X 1.9868
74 L X 2.7176
75 V X 2.7276
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, 1.9411 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 1.9411 View CSV PDB
model_5 1.4996 View CSV PDB
model_7 1.4694 View CSV PDB
model_11 1.3994 View CSV PDB
model_1 1.38 View CSV PDB
model_9 1.3786 View CSV PDB
model_3 1.3453 View CSV PDB
model_4 1.3284 View CSV PDB
CABS_average 1.3217 View CSV PDB
model_10 1.2933 View CSV PDB
model_2 1.2826 View CSV PDB
model_0 1.2334 View CSV PDB
model_8 1.2149 View CSV PDB
model_6 1.036 View CSV PDB