Project name: c234f7c51a52ba8 [mutate: VL45A]

Status: done

Started: 2020-04-05 14:00:51
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 VL45A
Energy difference between WT (input) and mutated protein (by FoldX) 0.641266 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                                                       (00:00:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:50)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:06)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:31)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:31)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:32)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:32)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:33)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:33)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:34)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:34)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:35)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:35)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:36)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:22:38)
[INFO]       Movie:    Creting movie with webm format                                              (00:24:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:16)
Show buried residues
Minimal score value
-2.9224
Maximal score value
3.2686
Average score
-0.4096
Total score value
-43.8229
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 1.9835
2 T A 0.3623
3 Q A -0.1095
4 P A -0.4529
5 P A -0.7945
6 S A -1.1712
7 T A -0.8146
8 S A -0.6561
9 G A -0.1518
10 T A 0.0000
11 P A -0.1428
12 G A -0.7658
13 Q A 0.0000
14 R A -1.9883
15 V A 0.0000
16 T A -0.5180
17 I A 0.0000
18 S A -0.1722
19 C A 0.0000
20 S A -0.0203
21 G A 0.1037
22 S A -0.3715
23 S A -0.3715
24 S A -0.8082
25 N A -0.9008
26 I A 0.5413
27 E A -0.7115
28 T A -0.7789
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A 0.6384
33 W A 0.0000
34 Y A 1.1253
35 Q A 0.0000
36 Q A -0.5264
37 L A -0.9942
38 P A -1.5108
39 G A -1.0200
40 T A -0.4459
41 A A -0.3073
42 P A -0.3753
43 K A -0.1009
44 L A 1.0788
45 L A 0.0000 mutated: VL45A
46 M A 0.0000
47 H A -0.9613
48 T A -1.4030
49 N A 0.0000
50 N A -1.9175
51 Q A -2.0917
52 R A -1.5663
53 P A -0.8514
54 S A -0.7922
55 G A -0.5036
56 V A -0.3256
57 P A -1.1076
58 D A -2.2657
59 R A -1.9533
60 F A 0.0000
61 S A -1.2006
62 G A 0.0000
63 S A -1.4145
64 R A -2.0366
65 S A -1.3252
66 G A -1.1251
67 T A -0.6696
68 S A -0.8842
69 A A 0.0000
70 S A -0.6227
71 L A 0.0000
72 A A -0.5100
73 I A -0.7980
74 G A -1.3057
75 G A -1.2400
76 L A -0.3071
77 Q A 0.0000
78 S A -0.4600
79 E A 0.0000
80 D A -2.4960
81 E A -2.9224
82 A A 0.0000
83 D A -1.2340
84 Y A 0.0000
85 F A 1.1997
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.1840
90 D A -1.5611
91 D A -1.6595
92 N A -1.4037
93 L A -0.0143
94 N A -1.2197
95 G A -0.0321
96 V A 1.7610
97 I A 2.7370
98 F A 3.2686
99 G A 1.6291
100 G A 0.8522
101 G A 0.0000
102 T A 0.0000
103 K A -1.7472
104 L A 0.0000
105 T A -1.1514
106 V A -0.2015
107 L A 0.9748
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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, -0.4096 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 -0.4096 View CSV PDB
model_10 -0.473 View CSV PDB
model_3 -0.481 View CSV PDB
model_0 -0.5018 View CSV PDB
model_8 -0.5025 View CSV PDB
model_4 -0.5028 View CSV PDB
model_6 -0.5047 View CSV PDB
model_11 -0.5526 View CSV PDB
model_9 -0.6101 View CSV PDB
model_5 -0.6173 View CSV PDB
model_2 -0.6284 View CSV PDB
model_7 -0.6524 View CSV PDB
input -0.6598 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018