Project name: HS_Trim1_dynamic2

Status: done

Started: 2024-04-29 02:06:13
Chain sequence(s) A: KVFDENYEQDKELLEQLYEQAKKEKDSEAKEDYIEDIKEFSEIQKKTYTRIAKEVPKELAEKLKKYAEDLVKYAKELIEKI
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                                                (00:02:39)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:09:38)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:09:39)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:09:39)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:09:39)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:09:40)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:09:40)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:09:40)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:09:40)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:09:41)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:09:41)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:09:41)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:09:42)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:09:42)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:09:44)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:44)
Show buried residues
Minimal score value
-4.3017
Maximal score value
0.0115
Average score
-2.1662
Total score value
-175.4653
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 K A -1.4511
2 V A -0.2097
3 F A 0.0000
4 D A -1.9405
5 E A -2.7317
6 N A -2.4462
7 Y A 0.0000
8 E A -2.9629
9 Q A -2.9530
10 D A -2.1281
11 K A -1.9850
12 E A -2.8293
13 L A -1.2211
14 L A 0.0000
15 E A -2.3741
16 Q A -2.4794
17 L A -1.3136
18 Y A 0.0000
19 E A -3.5034
20 Q A -3.4904
21 A A 0.0000
22 K A -3.2509
23 K A -3.9617
24 E A -3.7637
25 K A -4.2196
26 D A -4.2805
27 S A -3.5378
28 E A -3.7604
29 A A -3.3183
30 K A -3.8037
31 E A -3.9219
32 D A -3.7314
33 Y A -2.2484
34 I A -2.2886
35 E A -3.3356
36 D A -2.6794
37 I A 0.0000
38 K A -2.0952
39 E A -2.3159
40 F A -0.6601
41 S A 0.0000
42 E A -2.1760
43 I A 0.0115
44 Q A -1.0972
45 K A -2.3158
46 K A -2.0432
47 T A -1.2738
48 Y A 0.0000
49 T A -2.3718
50 R A -2.7314
51 I A -0.9807
52 A A 0.0000
53 K A -3.4317
54 E A -2.9238
55 V A -2.0930
56 P A -2.5578
57 K A -3.8804
58 E A -3.4793
59 L A -3.2508
60 A A -3.7704
61 E A -4.3017
62 K A -3.6406
63 L A 0.0000
64 K A -3.6069
65 K A -3.5884
66 Y A -2.5944
67 A A 0.0000
68 E A -3.1408
69 D A -2.3132
70 L A 0.0000
71 V A -1.6492
72 K A -2.0092
73 Y A -1.2311
74 A A 0.0000
75 K A -2.0287
76 E A -1.9862
77 L A -1.5778
78 I A -1.6904
79 E A -2.6127
80 K A -2.3563
81 I A -1.5795
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, -2.1662 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_11 -2.1662 View CSV PDB
model_0 -2.2382 View CSV PDB
model_5 -2.2939 View CSV PDB
model_3 -2.337 View CSV PDB
model_4 -2.3378 View CSV PDB
CABS_average -2.3579 View CSV PDB
model_7 -2.3621 View CSV PDB
model_9 -2.3822 View CSV PDB
model_2 -2.3862 View CSV PDB
model_8 -2.4009 View CSV PDB
model_10 -2.4163 View CSV PDB
model_1 -2.4482 View CSV PDB
input -2.5083 View CSV PDB
model_6 -2.5252 View CSV PDB