Project name: HS_Trim1_dynamic [mutate: KA46A]

Status: done

Started: 2024-04-29 01:49:37
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
Mutated residues KA46A
Energy difference between WT (input) and mutated protein (by FoldX) 0.245281 kcal/mol
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]       FoldX:    Building mutant model                                                       (00:02:21)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:36)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:09:32)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:09:32)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:09:33)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:09:33)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:09:33)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:09:33)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:09:34)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:09:34)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:09:34)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:09:34)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:09:35)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:09:35)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:09:35)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:09:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:39)
Show buried residues
Minimal score value
-4.1883
Maximal score value
0.5733
Average score
-2.0531
Total score value
-166.3008
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 -1.5170
2 V A -0.1195
3 F A -0.7065
4 D A -2.4938
5 E A -3.1888
6 N A -3.0133
7 Y A 0.0000
8 E A -3.8639
9 Q A -3.6113
10 D A 0.0000
11 K A -3.0286
12 E A -3.5749
13 L A -1.8462
14 L A 0.0000
15 E A -2.4207
16 Q A -2.5197
17 L A -1.4554
18 Y A 0.0000
19 E A -3.0553
20 Q A -2.9857
21 A A 0.0000
22 K A -3.8261
23 K A -3.8689
24 E A -3.9858
25 K A -4.1883
26 D A -4.1861
27 S A -3.3017
28 E A -3.7924
29 A A -3.2249
30 K A -3.8614
31 E A -4.0184
32 D A -3.7118
33 Y A -2.8416
34 I A -2.5726
35 E A -3.6859
36 D A -3.0663
37 I A 0.0000
38 K A -2.5064
39 E A -2.7479
40 F A -0.7572
41 S A 0.0000
42 E A -1.8241
43 I A 0.5733
44 Q A -0.2557
45 K A -1.2962
46 A A -0.4523 mutated: KA46A
47 T A -0.4128
48 Y A 0.0000
49 T A -2.0902
50 R A -2.6344
51 I A -1.3885
52 A A 0.0000
53 K A -3.4977
54 E A -2.6006
55 V A -1.2832
56 P A -1.7473
57 K A -3.3440
58 E A -3.5039
59 L A -2.6720
60 A A 0.0000
61 E A -3.9550
62 K A -3.6293
63 L A 0.0000
64 K A -3.8333
65 K A -3.4185
66 Y A -2.2206
67 A A 0.0000
68 E A -3.2604
69 D A -2.2079
70 L A 0.0000
71 V A -1.5273
72 K A -2.2634
73 Y A -1.3630
74 A A 0.0000
75 K A -2.1282
76 E A -2.0453
77 L A 0.0000
78 I A -1.4837
79 E A -2.5058
80 K A -2.0445
81 I A -0.4407
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, -2.0531 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 -2.0531 View CSV PDB
model_6 -2.1627 View CSV PDB
model_1 -2.181 View CSV PDB
model_10 -2.185 View CSV PDB
model_2 -2.2065 View CSV PDB
CABS_average -2.2971 View CSV PDB
model_3 -2.3224 View CSV PDB
model_4 -2.3491 View CSV PDB
model_9 -2.3755 View CSV PDB
model_5 -2.3852 View CSV PDB
model_0 -2.3917 View CSV PDB
model_11 -2.4406 View CSV PDB
input -2.4719 View CSV PDB
model_8 -2.5127 View CSV PDB