Project name: d565f544dc8168e [mutate: TS28A]

Status: done

Started: 2020-04-05 13:57:16
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 TS28A
Energy difference between WT (input) and mutated protein (by FoldX) -0.333643 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:04)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:04)
[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                                                       (00:00:51)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:54)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:12)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:17:34)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:17:35)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:17:35)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:17:35)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:17:36)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:17:36)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:17:36)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:17:36)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:17:37)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:17:37)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:17:37)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:17:38)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:17:38)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:17:39)
[INFO]       Movie:    Creting movie with webm format                                              (00:18:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:53)
Show buried residues
Minimal score value
-3.2705
Maximal score value
3.1586
Average score
-0.4476
Total score value
-47.8883
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 2.4045
2 T A 0.9155
3 Q A 0.0000
4 P A -0.3831
5 P A -0.5262
6 S A -0.6736
7 T A -0.4864
8 S A -0.6361
9 G A -0.5182
10 T A -0.3460
11 P A -0.5674
12 G A -0.9652
13 Q A -0.9207
14 R A 0.0000
15 V A 0.0000
16 T A -0.1942
17 I A 0.0000
18 S A -0.3155
19 C A 0.0000
20 S A 0.0395
21 G A 0.2222
22 S A 0.3442
23 S A 0.0722
24 S A -0.7473
25 N A -0.5921
26 I A 0.4930
27 E A -1.4370
28 S A -1.4370 mutated: TS28A
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.2368
35 Q A 0.0000
36 Q A -1.6084
37 L A 0.0000
38 P A -1.5263
39 G A -1.1534
40 T A -0.8871
41 A A -0.6890
42 P A -0.8464
43 K A -0.9336
44 L A -0.0626
45 V A 0.0000
46 M A 0.0000
47 H A -1.2628
48 T A -1.8351
49 N A -2.0564
50 N A -2.5403
51 Q A 0.0000
52 R A -2.6431
53 P A -1.6866
54 S A -0.7890
55 G A -0.8054
56 V A -0.2774
57 P A -0.2874
58 D A -0.3988
59 R A 0.0000
60 F A 0.8857
61 S A -0.2788
62 G A -1.0771
63 S A -1.6110
64 R A -2.6133
65 S A -1.6225
66 G A -1.3908
67 T A -0.8527
68 S A -0.6816
69 A A 0.0000
70 S A -0.7203
71 L A 0.0000
72 A A 0.2965
73 I A 0.5350
74 G A 0.0000
75 G A 0.3705
76 L A 1.2378
77 Q A 0.0000
78 S A -0.5391
79 E A -1.4819
80 D A -2.9214
81 E A -3.2705
82 A A 0.0000
83 D A -1.6619
84 Y A 0.0000
85 F A 0.3713
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A -0.6337
90 D A -2.4242
91 D A -2.8638
92 N A -2.0069
93 L A -0.0895
94 N A -0.8896
95 G A -0.2531
96 V A 1.4195
97 I A 3.1586
98 F A 3.0860
99 G A 1.1864
100 G A 0.3147
101 G A -0.6532
102 T A 0.0000
103 K A -1.5715
104 L A 0.0000
105 T A -1.2154
106 V A 0.0000
107 L A 0.8807
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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, -0.4476 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_1 -0.4476 View CSV PDB
model_10 -0.5089 View CSV PDB
model_9 -0.5346 View CSV PDB
model_8 -0.541 View CSV PDB
model_0 -0.581 View CSV PDB
model_11 -0.5927 View CSV PDB
model_3 -0.5933 View CSV PDB
model_5 -0.6034 View CSV PDB
model_4 -0.6306 View CSV PDB
model_2 -0.6425 View CSV PDB
model_6 -0.6689 View CSV PDB
input -0.6698 View CSV PDB
model_7 -0.6899 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018