Project name: 3b2deb14d9590d1

Status: done

Started: 2020-04-05 13:22:28
Settings
Chain sequence(s) A: QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGPIFGGGTKLTVL
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                                                (00:00:50)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:16:31)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:16:32)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:16:33)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:16:33)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:16:34)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:16:34)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:16:34)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:16:35)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:16:36)
[INFO]       Movie:    Creting movie with webm format                                              (00:18:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:06)
Show buried residues
Minimal score value
-3.1777
Maximal score value
1.913
Average score
-0.4931
Total score value
-54.2377
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 -0.7448
2 S A -0.6396
3 V A -0.2531
4 L A 0.0000
5 T A -0.3087
6 Q A -0.4956
7 P A -0.7834
8 P A -0.8095
9 S A -0.9717
10 A A 0.0000
11 S A -0.4496
12 G A 0.0000
13 T A 0.0547
14 P A -0.4411
15 G A -0.3625
16 Q A -0.5173
17 R A 0.0000
18 V A -0.1999
19 T A 0.0746
20 I A 0.0000
21 S A -0.4162
22 C A 0.0000
23 S A -0.4415
24 G A 0.0000
25 S A -0.4224
26 S A -0.3190
27 S A -0.6539
28 N A 0.0000
29 I A 0.0000
30 G A -0.7792
31 S A -0.8726
32 N A -1.1770
33 T A -1.1145
34 V A 0.0000
35 N A 0.0000
36 W A 0.0000
37 Y A 0.0000
38 Q A 0.0000
39 Q A -0.7011
40 L A -1.3082
41 P A -1.3851
42 G A -1.0016
43 T A -0.4341
44 A A -0.2806
45 P A -0.2816
46 K A -0.5255
47 L A -0.1727
48 L A 0.0000
49 I A 0.0000
50 Y A -0.1212
51 S A -1.1439
52 N A -2.1409
53 N A 0.0000
54 Q A -1.6740
55 R A -1.2093
56 P A -0.8421
57 S A -0.6429
58 G A -0.7702
59 V A -0.4208
60 P A -0.5252
61 D A -1.2418
62 R A 0.0000
63 F A 1.5106
64 S A 0.5017
65 G A 0.0888
66 S A -0.7159
67 K A -1.5560
68 S A -1.0615
69 G A -0.9310
70 T A -0.7590
71 S A -0.7913
72 A A 0.0000
73 S A -0.3994
74 L A 0.0000
75 A A 0.4588
76 I A 0.6503
77 S A 0.1690
78 G A -0.3661
79 L A 0.6117
80 Q A -0.1028
81 S A -0.5681
82 E A -1.3015
83 D A -2.7653
84 E A -3.1777
85 A A 0.0000
86 D A -1.9355
87 Y A 0.0000
88 Y A 0.0074
89 C A 0.0000
90 A A 0.0000
91 A A 0.0000
92 W A -1.2035
93 D A -2.6832
94 D A -2.8626
95 S A -1.7073
96 L A -1.1190
97 N A -1.1635
98 G A 0.0334
99 P A 0.7541
100 I A 1.9130
101 F A 1.1805
102 G A 0.0970
103 G A -0.7496
104 G A -0.9734
105 T A 0.0000
106 K A -2.4171
107 L A 0.0000
108 T A -1.3167
109 V A -0.4257
110 L A 0.7053
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, -0.4931 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 -0.4931 View CSV PDB
model_2 -0.5483 View CSV PDB
model_3 -0.5634 View CSV PDB
model_9 -0.5952 View CSV PDB
model_7 -0.6061 View CSV PDB
model_6 -0.6081 View CSV PDB
model_0 -0.637 View CSV PDB
model_8 -0.6443 View CSV PDB
model_4 -0.6448 View CSV PDB
model_5 -0.7092 View CSV PDB
input -0.7198 View CSV PDB
model_10 -0.7327 View CSV PDB
model_11 -0.7646 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018