Project name: 47b96179aa5f370

Status: done

Started: 2020-04-05 13:54:33
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                                        (00:19:58)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:59)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:00)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:00)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:01)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:02)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:03)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:03)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:05)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:05)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:09)
[INFO]       Movie:    Creting movie with webm format                                              (00:22:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:28)
Show buried residues
Minimal score value
-3.3659
Maximal score value
3.0211
Average score
-0.491
Total score value
-52.5349
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 1.2797
2 T A 0.2477
3 Q A -0.3746
4 P A -0.5994
5 P A -0.7751
6 S A -0.9101
7 T A -0.5241
8 S A -0.2240
9 G A -0.2388
10 T A -0.2821
11 P A -0.4905
12 G A -1.0191
13 Q A -1.4807
14 R A 0.0000
15 V A 0.0000
16 T A -0.3446
17 I A 0.0000
18 S A -0.4220
19 C A 0.0000
20 S A -0.2304
21 G A -0.1172
22 S A 0.1916
23 S A -0.2728
24 S A -0.5450
25 N A -0.9240
26 I A 0.6620
27 E A -1.2955
28 T A -1.5347
29 N A -1.1959
30 T A 0.0000
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.4829
35 Q A 0.0000
36 Q A -0.7775
37 L A -0.7018
38 P A -1.1576
39 G A -1.1927
40 T A 0.0000
41 A A -0.2281
42 P A -0.4026
43 K A -0.1485
44 L A 0.5105
45 V A 0.0000
46 M A -0.5839
47 H A 0.0000
48 T A 0.0000
49 N A -2.2972
50 N A -2.3843
51 Q A -1.7389
52 R A -1.4649
53 P A -0.9762
54 S A -0.8978
55 G A -0.7618
56 V A -0.6328
57 P A 0.0000
58 D A -2.6904
59 R A -2.7769
60 F A 0.0000
61 S A -1.3408
62 G A -0.8708
63 S A -0.6861
64 R A -0.4075
65 S A -0.3933
66 G A -0.2231
67 T A -0.2076
68 S A -0.5929
69 A A 0.0000
70 S A -0.4284
71 L A 0.0000
72 A A -0.5961
73 I A 0.0000
74 G A -1.7335
75 G A -1.4746
76 L A -0.9335
77 Q A -1.0449
78 S A 0.0000
79 E A 0.0000
80 D A -2.2681
81 E A -2.0870
82 A A 0.0000
83 D A -1.4073
84 Y A 0.0000
85 F A 0.1194
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.0000
90 D A -2.7703
91 D A -3.3659
92 N A -2.0542
93 L A -0.0955
94 N A -1.5169
95 G A -0.6748
96 V A 1.3870
97 I A 3.0211
98 F A 2.8908
99 G A 1.4013
100 G A 0.1687
101 G A -0.6447
102 T A 0.0000
103 K A -1.6548
104 L A 0.0000
105 T A -0.7286
106 V A -0.0508
107 L A 0.9689
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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, -0.491 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_5 -0.491 View CSV PDB
model_0 -0.5093 View CSV PDB
model_4 -0.5121 View CSV PDB
model_6 -0.5439 View CSV PDB
model_11 -0.5772 View CSV PDB
model_2 -0.5832 View CSV PDB
model_9 -0.5912 View CSV PDB
input -0.6701 View CSV PDB
model_7 -0.6826 View CSV PDB
model_1 -0.6896 View CSV PDB
model_10 -0.6944 View CSV PDB
model_8 -0.7462 View CSV PDB
model_3 -0.763 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018