Project name: 57894a1e4dbb816

Status: done

Started: 2020-04-05 13:54:36
Settings
Chain sequence(s) A: LTQPPSTSGTPGQRVTISCSGSSSNIETNTVNWYQQLPGTAPKLVMHTNNQRPSGVPDRFSGSRSGTSASLAIGGLQSEDEADYFCAAWDDNLNGVIFGGGTKLTVL
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                                                (00:00:35)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:19:42)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:43)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:19:43)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:19:44)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:19:44)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:19:45)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:19:45)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:19:46)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:19:46)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:19:47)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:19:47)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:19:48)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:19:48)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:19:52)
[INFO]       Movie:    Creting movie with webm format                                              (00:22:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:05)
Show buried residues
Minimal score value
-2.8732
Maximal score value
2.1879
Average score
-0.6701
Total score value
-71.6976
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 L A 1.1240
2 T A 0.1166
3 Q A -0.3357
4 P A -0.7738
5 P A -1.0684
6 S A -1.1980
7 T A -0.7383
8 S A -0.5022
9 G A -0.6530
10 T A -0.6018
11 P A -1.1569
12 G A -1.9255
13 Q A -2.6315
14 R A -2.8732
15 V A 0.0000
16 T A -0.6035
17 I A 0.0000
18 S A -0.3496
19 C A 0.0000
20 S A -0.2514
21 G A -0.2849
22 S A -0.3928
23 S A -0.8417
24 S A -0.9291
25 N A -1.1964
26 I A -0.6044
27 E A -1.7821
28 T A -1.0797
29 N A -1.1906
30 T A -0.6715
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A -0.1393
35 Q A 0.0000
36 Q A -0.9320
37 L A -0.6715
38 P A -0.5108
39 G A -0.5349
40 T A -0.5207
41 A A -0.4711
42 P A -0.7807
43 K A -1.1891
44 L A -0.3505
45 V A 0.0000
46 M A 0.0000
47 H A -1.2805
48 T A -1.2093
49 N A 0.0000
50 N A -2.3436
51 Q A -2.4873
52 R A -2.5875
53 P A -1.0819
54 S A -0.8697
55 G A -0.8853
56 V A -1.0392
57 P A -1.4579
58 D A -2.3403
59 R A -1.6812
60 F A 0.0000
61 S A -1.4626
62 G A 0.0000
63 S A -0.8344
64 R A -0.8080
65 S A -0.4949
66 G A -0.6552
67 T A -0.5360
68 S A -0.3676
69 A A 0.0000
70 S A -0.5366
71 L A 0.0000
72 A A -0.6801
73 I A 0.0000
74 G A -2.0256
75 G A -1.8467
76 L A 0.0000
77 Q A -2.3234
78 S A -1.6280
79 E A -2.4099
80 D A 0.0000
81 E A -1.9239
82 A A 0.0000
83 D A -1.3243
84 Y A 0.0000
85 F A 0.1894
86 C A 0.0000
87 A A 0.0000
88 A A 0.8796
89 W A 0.2994
90 D A -1.8884
91 D A -2.4199
92 N A -1.8436
93 L A -0.3032
94 N A -1.4183
95 G A -0.5282
96 V A 1.0126
97 I A 2.1076
98 F A 2.1879
99 G A 0.9785
100 G A -0.1651
101 G A -0.6175
102 T A 0.0000
103 K A -2.2509
104 L A 0.0000
105 T A -0.4713
106 V A -0.1895
107 L A 1.3602
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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, -0.6701 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
input -0.6701 View CSV PDB
model_1 -0.7296 View CSV PDB
model_3 -0.7398 View CSV PDB
model_0 -0.7707 View CSV PDB
model_6 -0.7791 View CSV PDB
model_8 -0.8093 View CSV PDB
model_9 -0.8389 View CSV PDB
model_4 -0.8823 View CSV PDB
model_5 -0.8863 View CSV PDB
model_11 -0.8934 View CSV PDB
model_7 -0.8967 View CSV PDB
model_2 -0.9147 View CSV PDB
model_10 -0.9767 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018