Project name: NbD1

Status: done

Started: 2021-03-01 10:39:07
Settings
Chain sequence(s) A: QVQLQESGGGSVQAGGSLRLSCAASGWTYSTATMGWYRQAPGKERELVSSIFSDENTYYKDSVKGRFTISRDAAKNTVYLQMNSLKPEDTAMYYCYIRPTTSLANWRWGQGTQVTVSS
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:12)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:19:10)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:19:11)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:19:11)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:19:12)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:19:12)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:19:13)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:13)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:19:14)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:19:14)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:19:16)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:19:16)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:19:17)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:19:17)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:19:17)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:18)
Show buried residues
Minimal score value
-3.8458
Maximal score value
1.4018
Average score
-0.7403
Total score value
-87.3599
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 Q A -1.1570
2 V A -0.8204
3 Q A -1.5082
4 L A 0.0000
5 Q A -1.6452
6 E A -1.3095
7 S A -1.3148
8 G A -1.5759
9 G A -1.4362
10 G A -1.2789
11 S A -0.8713
12 V A 0.0000
13 Q A -1.8519
14 A A -1.2390
15 G A -0.9515
16 G A -1.2193
17 S A -1.6398
18 L A 0.0000
19 R A -2.3644
20 L A 0.0000
21 S A -0.8950
22 C A 0.0000
23 A A -0.9778
24 A A 0.0000
25 S A -1.3948
26 G A -1.0999
27 W A 0.0000
28 T A 0.0668
29 Y A 0.0863
30 S A -0.0101
31 T A 0.1942
32 A A 0.0000
33 T A 0.0000
34 M A 0.0000
35 G A 0.0000
36 W A 0.0000
37 Y A -0.3577
38 R A 0.0000
39 Q A -2.1685
40 A A -2.2368
41 P A -2.2436
42 G A -2.5760
43 K A -3.6648
44 E A -3.8458
45 R A -3.2814
46 E A 0.0000
47 L A -0.3384
48 V A 0.0000
49 S A 0.0000
50 S A 0.0000
51 I A 0.0000
52 F A 0.2759
53 S A -0.4075
54 D A -1.3758
55 E A -1.6790
56 N A -0.5339
57 T A 0.5845
58 Y A 1.4018
59 Y A 0.6468
60 K A -0.9891
61 D A -1.0331
62 S A -0.5829
63 V A -0.6738
64 K A 0.0000
65 G A -1.5134
66 R A -2.3074
67 F A 0.0000
68 T A -0.4472
69 I A 0.0000
70 S A -0.3235
71 R A -0.6905
72 D A -1.8966
73 A A -1.1617
74 A A -1.1990
75 K A -2.0131
76 N A 0.0000
77 T A -1.0758
78 V A 0.0000
79 Y A -0.5817
80 L A 0.0000
81 Q A -1.9675
82 M A 0.0000
83 N A -2.0456
84 S A -1.4840
85 L A -1.7328
86 K A -2.3292
87 P A -1.5085
88 E A 0.0000
89 D A -2.3086
90 T A -1.3950
91 A A 0.0000
92 M A -0.6720
93 Y A 0.0000
94 Y A -0.1926
95 C A 0.0000
96 Y A 0.0000
97 I A 0.0000
98 R A 0.0000
99 P A -0.0534
100 T A 0.2506
101 T A -0.0027
102 S A 0.2918
103 L A 1.2371
104 A A 0.2626
105 N A -0.5478
106 W A 0.1581
107 R A -1.1517
108 W A -0.3432
109 G A -0.5889
110 Q A 0.0000
111 G A -0.8731
112 T A 0.0000
113 Q A -1.4635
114 V A 0.0000
115 T A -1.1279
116 V A -1.2336
117 S A -1.2001
118 S A -0.8358
Download PDB file
View in 3Dmol
Play the video

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, -0.7403 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_3 -0.7403 View CSV PDB
model_4 -0.7823 View CSV PDB
model_2 -0.8274 View CSV PDB
model_7 -0.8382 View CSV PDB
model_0 -0.8404 View CSV PDB
model_5 -0.8541 View CSV PDB
model_6 -0.8569 View CSV PDB
model_11 -0.8615 View CSV PDB
model_9 -0.864 View CSV PDB
model_1 -0.8748 View CSV PDB
input -0.8754 View CSV PDB
model_8 -0.9248 View CSV PDB
model_10 -0.9303 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018