Project name: 2AWT_Valen_d

Status: done

Started: 2020-02-17 14:22:53
Settings
Chain sequence(s) A: MADEKPKEGVKTENNDHINLKVAGQDGSVVQFKIKRHTPLSKLMKAYCERQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDVFQQQTGGVY
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:38)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:15:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:15:26)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:15:27)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:15:27)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:15:27)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:15:27)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:15:28)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:15:28)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:15:28)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:15:28)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:15:29)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:15:29)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:15:29)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:15:31)
[INFO]       Movie:    Creting movie with webm format                                              (00:17:17)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:19)
Show buried residues
Minimal score value
-3.8218
Maximal score value
1.0937
Average score
-1.459
Total score value
-138.6097
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 M A 0.1447
2 A A -1.2586
3 D A -2.5101
4 E A -2.7978
5 K A -3.6650
6 P A -3.2010
7 K A -3.5307
8 E A -2.7161
9 G A -1.5329
10 V A -0.1669
11 K A -1.4812
12 T A -2.0610
13 E A -2.7979
14 N A -2.9703
15 N A -2.9967
16 D A -3.6993
17 H A -3.8218
18 I A -2.8801
19 N A -2.6237
20 L A 0.0000
21 K A -1.8514
22 V A 0.0000
23 A A -0.6138
24 G A -0.7979
25 Q A -1.6323
26 D A -2.0197
27 G A -0.9335
28 S A 0.2408
29 V A 1.0937
30 V A 0.1205
31 Q A -1.2202
32 F A -0.7157
33 K A -1.7702
34 I A 0.0000
35 K A -2.7523
36 R A -3.3106
37 H A -2.7119
38 T A -1.9185
39 P A 0.0000
40 L A 0.0000
41 S A 0.0000
42 K A -1.7344
43 L A 0.0000
44 M A 0.0000
45 K A 0.0000
46 A A -2.5566
47 Y A -1.3579
48 C A -1.5346
49 E A -3.2487
50 R A -3.2634
51 Q A -2.2278
52 G A -0.9787
53 L A 0.0000
54 S A 0.0000
55 M A 0.0000
56 R A 0.0000
57 Q A -0.4519
58 I A 0.0000
59 R A -1.7155
60 F A 0.0000
61 R A -2.4961
62 F A -2.2957
63 D A -2.5837
64 G A -1.7736
65 Q A -1.9652
66 P A -2.0854
67 I A -1.9745
68 N A -2.5045
69 E A 0.0000
70 T A -1.5075
71 D A -2.1380
72 T A -1.6269
73 P A -1.3575
74 A A 0.0000
75 Q A -2.0610
76 L A 0.0000
77 E A -2.7156
78 M A 0.0000
79 E A -3.0763
80 D A -3.4614
81 E A -3.6705
82 D A -2.9349
83 T A -1.9949
84 I A 0.0000
85 D A -1.7284
86 V A 0.0000
87 F A -0.7998
88 Q A -1.2692
89 Q A -1.5951
90 Q A -1.4359
91 T A -0.9700
92 G A -0.7560
93 G A -0.2489
94 V A 0.5128
95 Y A 0.3329
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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, -1.459 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 -1.459 View CSV PDB
model_4 -1.4986 View CSV PDB
model_2 -1.5305 View CSV PDB
model_6 -1.5502 View CSV PDB
model_11 -1.5511 View CSV PDB
input -1.5581 View CSV PDB
model_7 -1.5946 View CSV PDB
model_9 -1.6045 View CSV PDB
model_5 -1.6338 View CSV PDB
model_1 -1.7136 View CSV PDB
model_10 -1.7753 View CSV PDB
model_0 -1.7784 View CSV PDB
model_8 -1.7887 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018