Project name: a2c98ddbe7352a1 [mutate: PV99A]

Status: done

Started: 2020-04-05 13:01:02
Settings
Chain sequence(s) A: QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGPIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues PV99A
Energy difference between WT (input) and mutated protein (by FoldX) 0.59474 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                                                       (00:01:10)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:11)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:27)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:00)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:02)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:02)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:02)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:03)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:03)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:05)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:06)
[INFO]       Movie:    Creting movie with webm format                                              (00:21:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:29)
Show buried residues
Minimal score value
-2.9286
Maximal score value
2.6778
Average score
-0.5417
Total score value
-59.5918
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 Q A -1.3680
2 S A 0.0000
3 V A 1.0019
4 L A 0.0000
5 T A 0.2626
6 Q A -0.4716
7 P A -0.7518
8 P A -0.7999
9 S A -1.0497
10 A A -0.7620
11 S A -0.5106
12 G A 0.0000
13 T A -0.1848
14 P A -0.2384
15 G A -0.7228
16 Q A 0.0000
17 R A -1.6787
18 V A -0.7705
19 T A -0.4908
20 I A 0.0000
21 S A -0.2645
22 C A 0.0000
23 S A -0.4754
24 G A -0.0567
25 S A -0.7867
26 S A -0.7220
27 S A -1.1323
28 N A -2.1434
29 I A 0.0000
30 G A -1.3537
31 S A -1.3149
32 N A 0.0000
33 T A -1.1721
34 V A 0.0000
35 N A 0.0000
36 W A 0.0000
37 Y A -0.2324
38 Q A 0.0000
39 Q A -1.6889
40 L A -1.5009
41 P A -1.2617
42 G A -0.8582
43 T A -0.6447
44 A A -0.5370
45 P A -0.7923
46 K A -0.7442
47 L A -0.1686
48 L A 0.0000
49 I A 0.0000
50 Y A -1.1257
51 S A -1.5139
52 N A -1.9296
53 N A -2.0811
54 Q A -2.2767
55 R A 0.0000
56 P A -1.4415
57 S A -0.8558
58 G A -0.2012
59 V A 0.6264
60 P A -0.0212
61 D A -1.7163
62 R A -1.1811
63 F A 0.0000
64 S A -0.7585
65 G A -0.7901
66 S A -0.7316
67 K A -1.1158
68 S A -0.9569
69 G A -0.9899
70 T A -0.8962
71 S A -0.7270
72 A A 0.0000
73 S A -0.4597
74 L A 0.0000
75 A A -0.4065
76 I A 0.0000
77 S A -0.8342
78 G A -0.4577
79 L A 0.5078
80 Q A 0.0000
81 S A 0.0796
82 E A -1.0698
83 D A -2.0954
84 E A -2.1195
85 A A 0.0000
86 D A -1.8951
87 Y A 0.0000
88 Y A -0.1268
89 C A 0.0000
90 A A 0.0000
91 A A 0.0000
92 W A -1.4636
93 D A -2.9286
94 D A -2.5268
95 S A -0.9638
96 L A 0.6280
97 N A -0.3861
98 G A 0.2521
99 V A 0.0000 mutated: PV99A
100 I A 2.6778
101 F A 2.5405
102 G A 0.7810
103 G A 0.0000
104 G A -1.0160
105 T A 0.0000
106 K A -1.9808
107 L A 0.0000
108 T A -0.5952
109 V A 0.2056
110 L A 1.1308
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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, -0.5417 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_6 -0.5417 View CSV PDB
model_3 -0.6218 View CSV PDB
model_1 -0.6478 View CSV PDB
input -0.6737 View CSV PDB
model_2 -0.6751 View CSV PDB
model_10 -0.6823 View CSV PDB
model_7 -0.7124 View CSV PDB
model_5 -0.7463 View CSV PDB
model_11 -0.7709 View CSV PDB
model_0 -0.7721 View CSV PDB
model_8 -0.7809 View CSV PDB
model_9 -0.8373 View CSV PDB
model_4 -0.8709 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018