Project name: a8eddf7a3d993bb [mutate: NS92A]

Status: done

Started: 2020-04-05 14:04:31
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 NS92A
Energy difference between WT (input) and mutated protein (by FoldX) -0.034921 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                                                       (00:00:39)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:18)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:46)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:17)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:17)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:18)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:18)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:18)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:19)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:19)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:19)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:20)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:20)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:20)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:21)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:21)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:22:25)
[INFO]       Movie:    Creting movie with webm format                                              (00:24:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:03)
Show buried residues
Minimal score value
-3.0326
Maximal score value
3.6297
Average score
-0.4018
Total score value
-42.9893
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 1.7866
2 T A 0.5180
3 Q A 0.0000
4 P A -0.7741
5 P A -1.1497
6 S A -1.0443
7 T A 0.0000
8 S A -0.4074
9 G A -0.3480
10 T A -0.2423
11 P A -0.6608
12 G A -1.0853
13 Q A -1.3220
14 R A -0.6329
15 V A -0.0412
16 T A 0.0268
17 I A 0.0000
18 S A -0.2420
19 C A 0.0000
20 S A -0.2903
21 G A 0.0000
22 S A -0.0405
23 S A -0.6567
24 S A -0.9187
25 N A -0.7660
26 I A 0.5968
27 E A -1.6236
28 T A 0.0000
29 N A -1.7039
30 T A 0.0000
31 V A 0.0000
32 N A 0.4283
33 W A 0.0000
34 Y A 0.8123
35 Q A 0.0000
36 Q A -1.4082
37 L A -1.4141
38 P A -1.6783
39 G A -1.6159
40 T A -0.6492
41 A A 0.1037
42 P A 0.1110
43 K A 0.0000
44 L A 1.4719
45 V A 0.0000
46 M A 0.0000
47 H A -1.4145
48 T A -1.7899
49 N A -2.4820
50 N A -2.1828
51 Q A -2.2772
52 R A -1.8374
53 P A -1.0538
54 S A -0.4835
55 G A -0.1915
56 V A 1.1969
57 P A 0.0000
58 D A -1.6683
59 R A 0.0000
60 F A -0.5529
61 S A -0.6065
62 G A -1.0203
63 S A -0.8293
64 R A -1.0526
65 S A -0.8306
66 G A -0.9062
67 T A -0.5165
68 S A -0.5294
69 A A 0.0000
70 S A -0.4396
71 L A 0.0000
72 A A -0.0521
73 I A 0.0000
74 G A -0.6231
75 G A -0.7006
76 L A 0.0000
77 Q A 0.0000
78 S A -0.7920
79 E A 0.0000
80 D A -2.6188
81 E A -3.0326
82 A A 0.0000
83 D A -1.9806
84 Y A 0.0000
85 F A 0.3070
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.3832
90 D A -1.3792
91 D A -1.4675
92 S A -0.7395 mutated: NS92A
93 L A 0.4772
94 N A -0.8970
95 G A 0.3668
96 V A 2.7202
97 I A 3.6297
98 F A 3.2743
99 G A 0.9368
100 G A 0.1831
101 G A -1.0779
102 T A 0.0000
103 K A -2.5594
104 L A 0.0000
105 T A -1.0154
106 V A -0.4927
107 L A 0.4887
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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, -0.4018 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 -0.4018 View CSV PDB
model_10 -0.4289 View CSV PDB
model_3 -0.4291 View CSV PDB
model_1 -0.4442 View CSV PDB
model_4 -0.4595 View CSV PDB
model_9 -0.476 View CSV PDB
model_8 -0.4768 View CSV PDB
model_11 -0.4793 View CSV PDB
model_2 -0.488 View CSV PDB
model_6 -0.5644 View CSV PDB
model_7 -0.6207 View CSV PDB
input -0.6308 View CSV PDB
model_5 -0.6904 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018