Project name: 7aeaf22dc6cc960 [mutate: TA7A]

Status: done

Started: 2020-04-05 14:00:22
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 TA7A
Energy difference between WT (input) and mutated protein (by FoldX) 0.562518 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                                                       (00:00:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:38)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:54)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:30)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:31)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:31)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:32)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:33)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:33)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:34)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:34)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:34)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:37)
[INFO]       Movie:    Creting movie with webm format                                              (00:23:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:23)
Show buried residues
Minimal score value
-3.4714
Maximal score value
3.2236
Average score
-0.5256
Total score value
-56.2368
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 1.1531
2 T A 0.1448
3 Q A 0.0000
4 P A -0.9708
5 P A -1.0051
6 S A -1.2635
7 A A -1.0902 mutated: TA7A
8 S A -0.8641
9 G A -0.8837
10 T A -0.5276
11 P A -0.5183
12 G A -1.0748
13 Q A -1.6028
14 R A -2.3880
15 V A 0.0000
16 T A -0.7591
17 I A 0.0000
18 S A -0.4544
19 C A 0.0000
20 S A -0.2634
21 G A 0.0000
22 S A -0.2044
23 S A -0.3404
24 S A -0.6926
25 N A -0.5319
26 I A 0.5008
27 E A -1.4925
28 T A -1.2680
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A -0.1246
33 W A 0.0000
34 Y A 0.9274
35 Q A 0.0000
36 Q A -0.3689
37 L A -0.5303
38 P A -0.8622
39 G A -0.4920
40 T A -0.3862
41 A A -0.2539
42 P A -0.0422
43 K A 0.5444
44 L A 1.5399
45 V A 0.0000
46 M A 0.0000
47 H A -1.9707
48 T A 0.0000
49 N A -2.5475
50 N A -3.2805
51 Q A -3.4714
52 R A -3.2838
53 P A -2.1752
54 S A -1.5631
55 G A -1.0292
56 V A 0.7491
57 P A -0.0556
58 D A -1.4332
59 R A -2.4595
60 F A 0.0000
61 S A -1.8940
62 G A -1.7876
63 S A -1.2890
64 R A -2.0417
65 S A -1.3372
66 G A -1.0592
67 T A -0.8586
68 S A -0.8064
69 A A 0.0000
70 S A -0.7789
71 L A 0.0000
72 A A -0.8741
73 I A 0.0000
74 G A -1.8457
75 G A -1.4081
76 L A -0.7201
77 Q A -0.4526
78 S A -0.3990
79 E A 0.0000
80 D A -1.9803
81 E A -1.8120
82 A A 0.0000
83 D A -1.2191
84 Y A 0.0000
85 F A 0.4439
86 C A 0.0000
87 A A 1.3686
88 A A 0.0000
89 W A 1.1572
90 D A 0.0000
91 D A -0.9823
92 N A -1.2239
93 L A 0.1738
94 N A -0.7218
95 G A 0.5026
96 V A 2.8103
97 I A 3.2236
98 F A 2.1085
99 G A 0.3428
100 G A 0.0289
101 G A -0.9025
102 T A 0.0000
103 K A -2.4271
104 L A 0.0000
105 T A -1.2803
106 V A 0.0000
107 L A 0.6706
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View in 3Dmol
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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, -0.5256 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_4 -0.5256 View CSV PDB
model_5 -0.5806 View CSV PDB
model_8 -0.583 View CSV PDB
model_10 -0.6412 View CSV PDB
model_11 -0.6417 View CSV PDB
model_9 -0.6666 View CSV PDB
input -0.6677 View CSV PDB
model_6 -0.6834 View CSV PDB
model_1 -0.6921 View CSV PDB
model_3 -0.7006 View CSV PDB
model_7 -0.7018 View CSV PDB
model_0 -0.7088 View CSV PDB
model_2 -0.7523 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018