Project name: 555630d1193757c [mutate: AT10A]

Status: done

Started: 2020-04-05 13:19:46
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 AT10A
Energy difference between WT (input) and mutated protein (by FoldX) 0.0293454 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:04)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:04)
[INFO]       FoldX:    Building mutant model                                                       (00:01:05)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:05)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:23)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:17:27)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:17:28)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:17:29)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:17:30)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:17:30)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:17:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:17:33)
[INFO]       Movie:    Creting movie with webm format                                              (00:18:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:00)
Show buried residues
Minimal score value
-3.5449
Maximal score value
1.9217
Average score
-0.5725
Total score value
-62.9785
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 -1.0053
2 S A -0.2554
3 V A 0.8698
4 L A 0.0000
5 T A 0.1048
6 Q A 0.0000
7 P A -0.6064
8 P A -0.8972
9 S A -1.3156
10 T A -0.9088 mutated: AT10A
11 S A -0.6014
12 G A 0.0000
13 T A -0.4625
14 P A -0.6770
15 G A -1.3791
16 Q A -2.0441
17 R A -1.9504
18 V A 0.0000
19 T A -0.6638
20 I A 0.0000
21 S A -0.5652
22 C A 0.0000
23 S A -0.4795
24 G A 0.0000
25 S A -0.1313
26 S A -0.4754
27 S A -0.5611
28 N A -0.5544
29 I A -0.7840
30 G A -1.1988
31 S A -0.9013
32 N A -0.7302
33 T A -0.1600
34 V A 0.0000
35 N A 0.6199
36 W A 0.0000
37 Y A 0.8378
38 Q A 0.0000
39 Q A -1.6244
40 L A 0.0000
41 P A -1.8054
42 G A -1.2043
43 T A -0.5762
44 A A -0.3601
45 P A -0.4509
46 K A 0.0000
47 L A 1.3586
48 L A 0.0000
49 I A 0.0000
50 Y A 0.4659
51 S A -0.5286
52 N A -1.9807
53 N A -2.2926
54 Q A -2.0176
55 R A -0.9260
56 P A -0.6510
57 S A -0.2885
58 G A -0.5667
59 V A 0.0000
60 P A -1.2589
61 D A -2.0093
62 R A 0.0000
63 F A 0.0000
64 S A -1.1211
65 G A -1.1949
66 S A -1.4499
67 K A -2.1834
68 S A -1.4340
69 G A -1.1758
70 T A -0.9530
71 S A -1.0177
72 A A 0.0000
73 S A -0.9732
74 L A 0.0000
75 A A -0.3870
76 I A 0.0000
77 S A -1.3192
78 G A -1.7096
79 L A 0.0000
80 Q A -1.6580
81 S A -1.1379
82 E A 0.0000
83 D A -2.7320
84 E A -3.5449
85 A A 0.0000
86 D A -1.9850
87 Y A 0.0000
88 Y A 0.3099
89 C A 0.0000
90 A A 0.0000
91 A A 0.0000
92 W A 1.0667
93 D A -0.6300
94 D A -1.5479
95 S A -0.6524
96 L A 0.4067
97 N A -0.8312
98 G A -0.3651
99 P A 0.0695
100 I A 0.0000
101 F A 1.9217
102 G A 0.8504
103 G A 0.2984
104 G A -0.4130
105 T A 0.0000
106 K A -2.4751
107 L A 0.0000
108 T A -1.2944
109 V A -0.8480
110 L A 0.7245
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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, -0.5725 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_0 -0.5725 View CSV PDB
model_7 -0.6359 View CSV PDB
model_2 -0.6719 View CSV PDB
model_9 -0.7064 View CSV PDB
input -0.7148 View CSV PDB
model_10 -0.7173 View CSV PDB
model_4 -0.7705 View CSV PDB
model_3 -0.805 View CSV PDB
model_8 -0.8079 View CSV PDB
model_6 -0.824 View CSV PDB
model_5 -0.8521 View CSV PDB
model_11 -0.8872 View CSV PDB
model_1 -0.9289 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018