Project name: 9efd81c46631c77 [mutate: VP96A]

Status: done

Started: 2020-04-05 14:04:59
Settings
Chain sequence(s) A: LTQPPSTSGTPGQRVTISCSGSSSNIETNTVNWYQQLPGTAPKLVMHTNNQRPSGVPDRFSGSRSGTSASLAIGGLQSEDEADYFCAAWDDNLNGVIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues VP96A
Energy difference between WT (input) and mutated protein (by FoldX) -0.0581383 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 minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:00:39)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:30)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:45)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:22)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:22)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:23)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:23)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:24)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:24)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:24)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:25)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:25)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:25)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:26)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:26)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:26)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:22:30)
[INFO]       Movie:    Creting movie with webm format                                              (00:24:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:02)
Show buried residues
Minimal score value
-2.9708
Maximal score value
2.4473
Average score
-0.4716
Total score value
-50.4577
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 L A 1.8634
2 T A 0.9089
3 Q A -0.1373
4 P A -0.6837
5 P A -0.9281
6 S A -1.1364
7 T A -0.8220
8 S A -0.4328
9 G A 0.0000
10 T A -0.7278
11 P A -1.0473
12 G A -1.6045
13 Q A -2.4343
14 R A -2.3106
15 V A -1.2409
16 T A -0.6855
17 I A 0.0000
18 S A -0.3336
19 C A 0.0000
20 S A -0.0693
21 G A 0.0000
22 S A 0.0002
23 S A -0.3743
24 S A -0.5916
25 N A -0.7468
26 I A 1.0069
27 E A 0.0000
28 T A -0.8000
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A 0.3249
33 W A 0.0000
34 Y A 0.4590
35 Q A 0.0000
36 Q A -0.4256
37 L A -0.1755
38 P A -0.5944
39 G A -0.3624
40 T A -0.3028
41 A A -0.0269
42 P A -0.2062
43 K A -0.4870
44 L A 0.5920
45 V A 0.0000
46 M A 0.0000
47 H A -1.2759
48 T A 0.0000
49 N A -1.9937
50 N A -2.7430
51 Q A -2.9708
52 R A -2.8289
53 P A -1.0508
54 S A -0.5497
55 G A -0.1391
56 V A 0.4471
57 P A -0.4765
58 D A -1.3158
59 R A 0.0811
60 F A 1.2828
61 S A 0.1797
62 G A 0.0000
63 S A -1.3201
64 R A -1.4318
65 S A -0.7805
66 G A -0.6120
67 T A -0.5629
68 S A -0.6279
69 A A 0.0000
70 S A -0.5008
71 L A 0.0000
72 A A -0.0729
73 I A 0.0000
74 G A -0.9275
75 G A -0.7963
76 L A -0.3323
77 Q A -1.3037
78 S A -1.7263
79 E A -2.6640
80 D A -2.9540
81 E A -2.6360
82 A A 0.0000
83 D A -1.2577
84 Y A 0.0000
85 F A 0.3804
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.3824
90 D A -0.9029
91 D A -1.7531
92 N A -0.8087
93 L A 0.1226
94 N A -1.2746
95 G A -0.4739
96 P A 0.2879 mutated: VP96A
97 I A 1.6110
98 F A 2.4473
99 G A 1.3333
100 G A 0.2741
101 G A -0.7264
102 T A 0.0000
103 K A -2.3177
104 L A 0.0000
105 T A -1.1874
106 V A 0.0000
107 L A 0.5405
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.4716 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 A3D Score
model_10 -0.4716 View CSV PDB
model_5 -0.4869 View CSV PDB
model_2 -0.4895 View CSV PDB
model_7 -0.533 View CSV PDB
model_8 -0.5682 View CSV PDB
model_9 -0.5912 View CSV PDB
model_1 -0.6216 View CSV PDB
model_6 -0.6352 View CSV PDB
model_4 -0.6646 View CSV PDB
model_11 -0.6653 View CSV PDB
input -0.683 View CSV PDB
model_3 -0.6956 View CSV PDB
model_0 -0.7237 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018