Project name: Nucleocapsid Nterminal

Status: done

Started: 2020-06-22 22:41:30
Settings
Chain sequence(s) A: GAMGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGS
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                                                (00:01:37)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:39:34)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:39:35)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:39:36)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:39:37)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:39:38)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:39:39)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:39:40)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:39:41)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:39:42)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:39:43)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:39:44)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:39:45)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:39:46)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:40:02)
[INFO]       Movie:    Creting movie with webm format                                              (00:48:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:48:05)
Show buried residues
Minimal score value
-3.103
Maximal score value
1.8136
Average score
-0.7266
Total score value
-101.7247
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 G A -0.5382
2 A A 0.0302
3 M A 0.7527
4 G A 0.7417
5 L A 0.8054
6 P A -0.4216
7 N A -1.6402
8 N A -1.5247
9 T A -0.7761
10 A A -0.2158
11 S A -0.3431
12 W A 0.5089
13 F A 0.0000
14 T A 0.3769
15 A A 0.0000
16 L A 0.0000
17 T A 0.0000
18 Q A 0.0000
19 H A -0.8926
20 G A -1.2269
21 K A -1.2881
22 E A 0.0000
23 D A 0.0000
24 L A 0.0000
25 K A -2.0118
26 F A 0.0000
27 P A -1.9111
28 R A -2.5198
29 G A -1.9394
30 Q A -2.3717
31 G A 0.0000
32 V A 0.0000
33 P A 0.0000
34 I A 0.3641
35 N A -0.9296
36 T A -1.0261
37 N A -2.2776
38 S A -1.5924
39 S A -1.6787
40 P A -1.2177
41 D A -1.9919
42 D A 0.0000
43 Q A 0.0000
44 I A 0.0000
45 G A 0.0000
46 Y A 0.0000
47 Y A 0.0000
48 R A -1.0833
49 R A -1.4061
50 A A -0.9630
51 T A -1.0532
52 R A 0.0000
53 R A -1.9817
54 I A -0.8556
55 R A -2.3378
56 G A -1.8931
57 G A -1.8262
58 D A -2.5596
59 G A -1.6812
60 K A -1.4629
61 M A -0.4462
62 K A -0.9857
63 D A -1.5708
64 L A 0.0229
65 S A -0.3305
66 P A 0.0000
67 R A -1.3375
68 W A 0.0000
69 Y A -0.1693
70 F A 0.0000
71 Y A 0.0000
72 Y A 0.0000
73 L A 0.0000
74 G A -1.1357
75 T A -0.5896
76 G A -0.7939
77 P A -0.8507
78 E A -0.5714
79 A A -0.2505
80 G A -0.1342
81 L A 0.3763
82 P A 0.0691
83 Y A -0.1370
84 G A -1.0953
85 A A 0.0000
86 N A -2.0174
87 K A -2.0453
88 D A -1.8662
89 G A 0.0000
90 I A 0.0000
91 I A 0.0000
92 W A 0.0000
93 V A 0.0000
94 A A 0.0000
95 T A 0.0000
96 E A -2.4796
97 G A -1.4916
98 A A -0.8405
99 L A -0.5449
100 N A -1.0377
101 T A 0.0000
102 P A -1.1082
103 K A 0.0000
104 D A -1.7152
105 H A -0.7491
106 I A 0.2394
107 G A -0.3566
108 T A -1.2038
109 R A -2.6135
110 N A -2.8330
111 P A -1.7431
112 A A -1.5293
113 N A -3.0219
114 N A -3.1030
115 A A 0.0000
116 A A -1.1602
117 I A 0.2942
118 V A 0.9913
119 L A 1.8136
120 Q A 1.0570
121 L A 0.6148
122 P A -0.1560
123 Q A -1.2836
124 G A -1.1567
125 T A -0.9701
126 T A -0.6546
127 L A -0.5421
128 P A -1.0066
129 K A -1.3012
130 G A -0.8376
131 F A 0.4826
132 Y A 1.1724
133 A A 0.5365
134 E A -0.2682
135 G A -0.4831
136 S A -1.8302
137 R A -2.9197
138 G A -2.5455
139 G A -2.0116
140 S A -1.7107
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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, -0.7266 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 -0.7266 View CSV PDB
model_4 -0.7996 View CSV PDB
model_5 -0.8055 View CSV PDB
model_3 -0.9447 View CSV PDB
model_11 -0.9681 View CSV PDB
model_7 -0.9781 View CSV PDB
model_1 -0.999 View CSV PDB
model_8 -1.0309 View CSV PDB
model_10 -1.0523 View CSV PDB
model_2 -1.0846 View CSV PDB
input -1.1145 View CSV PDB
model_9 -1.1195 View CSV PDB
model_6 -1.1333 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018