Project name: 498fe6597a11e1e

Status: done

Started: 2020-04-05 13:22:01
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                                                (00:00:51)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:16:04)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:16:04)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:16:07)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:16:07)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:16:07)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:16:08)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:16:08)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:16:10)
[INFO]       Movie:    Creting movie with webm format                                              (00:17:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:42)
Show buried residues
Minimal score value
-2.5257
Maximal score value
2.4109
Average score
-0.4848
Total score value
-53.3258
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 -0.4833
2 S A 0.0000
3 V A 2.1619
4 L A 0.0000
5 T A 0.3360
6 Q A 0.0000
7 P A -0.7548
8 P A -0.8068
9 S A -1.0892
10 A A 0.0000
11 S A -0.7368
12 G A 0.0000
13 T A -0.6512
14 P A -0.8348
15 G A -1.3440
16 Q A -1.9296
17 R A -2.3765
18 V A 0.0000
19 T A -0.6040
20 I A 0.0000
21 S A -0.3840
22 C A 0.0000
23 S A -0.3144
24 G A -0.0107
25 S A -0.1606
26 S A -0.5781
27 S A -0.9050
28 N A -1.3452
29 I A 0.0000
30 G A -1.6427
31 S A 0.0000
32 N A -2.5257
33 T A -1.8486
34 V A 0.0000
35 N A 0.2955
36 W A 0.0000
37 Y A 0.6901
38 Q A 0.0000
39 Q A -0.8075
40 L A 0.0000
41 P A -1.2667
42 G A -0.8471
43 T A -0.5971
44 A A -0.2369
45 P A -0.3626
46 K A 0.0348
47 L A 1.3147
48 L A 0.0000
49 I A 0.2850
50 Y A -0.3794
51 S A -1.2003
52 N A -1.9548
53 N A -1.8909
54 Q A -1.8714
55 R A 0.0000
56 P A -0.5490
57 S A -0.2178
58 G A -0.1280
59 V A 0.5846
60 P A 0.0000
61 D A -1.7807
62 R A 0.0000
63 F A 0.0000
64 S A -0.9145
65 G A 0.0000
66 S A -1.6298
67 K A -2.3978
68 S A -1.4436
69 G A -1.3143
70 T A -1.2388
71 S A -1.1159
72 A A 0.0000
73 S A -0.8103
74 L A 0.0000
75 A A -0.6387
76 I A 0.0000
77 S A -1.2716
78 G A -0.8895
79 L A 0.0000
80 Q A -0.0762
81 S A -0.1850
82 E A 0.0000
83 D A -2.1943
84 E A -2.3081
85 A A 0.0000
86 D A -1.7760
87 Y A 0.0000
88 Y A 0.0785
89 C A 0.0000
90 A A 0.3425
91 A A 0.0000
92 W A -0.4746
93 D A -2.0296
94 D A -2.3063
95 S A -1.0224
96 L A 0.2852
97 N A -0.4145
98 G A 0.0477
99 P A 0.9924
100 I A 2.4109
101 F A 1.7101
102 G A 0.5695
103 G A -0.1098
104 G A -0.9764
105 T A 0.0000
106 K A -2.2969
107 L A 0.0000
108 T A -1.1069
109 V A -0.0691
110 L A 0.9619
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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, -0.4848 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_6 -0.4848 View CSV PDB
model_2 -0.5462 View CSV PDB
model_9 -0.5641 View CSV PDB
model_3 -0.5711 View CSV PDB
model_7 -0.5713 View CSV PDB
model_0 -0.6215 View CSV PDB
model_8 -0.629 View CSV PDB
model_4 -0.6464 View CSV PDB
model_11 -0.6604 View CSV PDB
model_1 -0.699 View CSV PDB
model_10 -0.7115 View CSV PDB
input -0.7198 View CSV PDB
model_5 -0.7337 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018