Project name: Nsp9 1 Subunit

Status: done

Started: 2020-06-22 22:49:51
Settings
Chain sequence(s) A: NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTPKGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
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]       CABS:     Running CABS flex simulation                                                (00:02:02)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:13)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:14)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:29:16)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:29:17)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:29:18)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:18)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:28)
[INFO]       Movie:    Creting movie with webm format                                              (00:34:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:34:11)
Show buried residues
Minimal score value
-2.9382
Maximal score value
1.1557
Average score
-0.6194
Total score value
-69.993
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 N A -1.9903
2 N A -1.8665
3 E A -0.9704
4 L A 0.0000
5 S A -0.1220
6 P A -0.1813
7 V A 0.6854
8 A A 0.1536
9 L A -0.0342
10 R A -1.6492
11 Q A -1.3578
12 M A -0.3117
13 S A -0.1754
14 C A 0.0000
15 A A -0.9421
16 A A 0.0000
17 G A -0.7824
18 T A 0.0000
19 T A -0.7714
20 Q A -1.5530
21 T A -0.9085
22 A A -0.3903
23 C A -0.5694
24 T A -0.7403
25 D A -1.7221
26 D A -2.0916
27 N A 0.0000
28 A A 0.0000
29 L A 0.4819
30 A A 0.0000
31 Y A 0.0000
32 Y A 0.0000
33 N A 0.0000
34 T A -1.0387
35 T A -1.5093
36 K A -2.2134
37 G A -1.6625
38 G A -1.0939
39 R A 0.0000
40 F A 0.4347
41 V A 0.0000
42 L A 0.0000
43 A A 0.0000
44 L A 0.0000
45 L A 0.3583
46 S A 0.0000
47 D A -0.1285
48 L A 0.6557
49 Q A -0.7918
50 D A -1.0702
51 L A 0.0000
52 K A -1.2436
53 W A -0.0637
54 A A 0.0000
55 R A -0.3779
56 F A 0.0000
57 P A -0.5623
58 K A -1.0138
59 S A -1.0749
60 D A -1.6452
61 G A -1.5459
62 T A -1.1753
63 G A -0.6107
64 T A -0.2028
65 I A 0.6342
66 Y A 1.1557
67 T A 0.0000
68 E A -1.2866
69 L A 0.0000
70 E A -2.4097
71 P A -1.6086
72 P A -1.0177
73 C A -0.6375
74 R A -1.1630
75 F A -0.7255
76 V A -0.8500
77 T A -1.4194
78 D A -2.0863
79 T A -1.6697
80 P A -1.5261
81 K A -2.3079
82 G A -1.7231
83 P A -1.5429
84 K A -1.2227
85 V A -0.1762
86 K A -0.3411
87 Y A -0.3433
88 L A 0.0000
89 Y A -0.8964
90 F A 0.0000
91 I A 0.0000
92 K A -2.9382
93 G A -1.4704
94 L A -0.9821
95 N A -1.7919
96 N A -1.1626
97 L A 0.6305
98 N A 0.0000
99 R A -0.3179
100 G A 0.1405
101 M A 1.0294
102 V A 0.0000
103 L A 0.4376
104 G A -0.0856
105 S A 0.4050
106 L A 0.0000
107 A A -0.1691
108 A A -0.1608
109 T A -0.1523
110 V A -0.3122
111 R A -1.6826
112 L A -1.2349
113 Q A -1.6269
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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, -0.6194 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_2 -0.6194 View CSV PDB
model_4 -0.7031 View CSV PDB
model_10 -0.7246 View CSV PDB
model_7 -0.7683 View CSV PDB
model_0 -0.7734 View CSV PDB
model_9 -0.7762 View CSV PDB
model_3 -0.8019 View CSV PDB
model_6 -0.8025 View CSV PDB
model_8 -0.8033 View CSV PDB
model_5 -0.8146 View CSV PDB
model_1 -0.8403 View CSV PDB
model_11 -0.8921 View CSV PDB
input -0.9102 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018