Project name: 40d89cb2aab77f9

Status: done

Started: 2020-04-05 16:21:55
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Chain sequence(s) A: QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNAWVFGGGTKLTVLG
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:48)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:16:02)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:16:02)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:16:03)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:16:03)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:16:04)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:16:04)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:16:04)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:16:05)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:16:06)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:16:09)
[INFO]       Movie:    Creting movie with webm format                                              (00:17:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:17:24)
Show buried residues
Minimal score value
-3.1958
Maximal score value
2.5092
Average score
-0.5242
Total score value
-58.1852
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 -0.2585
2 S A 0.5490
3 V A 1.7631
4 L A 0.0000
5 T A 0.3315
6 Q A 0.0000
7 P A -0.7465
8 P A -0.8506
9 S A -1.0701
10 A A 0.0000
11 S A -0.5432
12 G A 0.0000
13 T A 0.0171
14 P A -0.3367
15 G A -0.9430
16 Q A -0.9863
17 R A -1.8116
18 V A -0.6786
19 T A -0.4598
20 I A 0.0000
21 S A -0.2366
22 C A 0.0000
23 S A -0.2257
24 G A 0.2254
25 S A -0.0403
26 S A -0.6008
27 S A -0.8358
28 N A 0.0000
29 I A 0.0000
30 G A -1.0476
31 S A -1.1789
32 N A -1.3736
33 T A -1.3324
34 V A 0.0000
35 N A 0.0000
36 W A 0.0000
37 Y A 0.9704
38 Q A 0.0000
39 Q A -1.2230
40 L A 0.0000
41 P A -2.0215
42 G A -1.8775
43 T A -1.2728
44 A A -0.2895
45 P A -0.3727
46 K A 0.1510
47 L A 1.1964
48 L A 0.0000
49 I A 0.0000
50 Y A -0.6064
51 S A -1.2767
52 N A -2.3307
53 N A -2.7535
54 Q A -2.6749
55 R A -2.3004
56 P A -1.1201
57 S A -0.7850
58 G A -0.4692
59 V A -0.2835
60 P A -0.4853
61 D A -1.0465
62 R A -1.7579
63 F A 0.0000
64 S A -1.1249
65 G A 0.0000
66 S A -0.8205
67 K A -1.2954
68 S A -1.0483
69 G A -1.0508
70 T A -0.8430
71 S A -0.7590
72 A A 0.0000
73 S A -0.4458
74 L A 0.0000
75 A A -0.7317
76 I A 0.0000
77 S A -1.0685
78 G A -0.6712
79 L A 0.2239
80 Q A 0.0000
81 S A -1.5003
82 E A -2.7856
83 D A -3.1958
84 E A -3.1707
85 A A 0.0000
86 D A -1.8323
87 Y A 0.0000
88 Y A 0.6282
89 C A 0.0000
90 A A 0.0000
91 A A 0.0000
92 W A 0.1116
93 D A 0.0000
94 D A -1.8478
95 S A -0.7566
96 L A 0.4435
97 N A -0.9953
98 A A 0.0366
99 W A 1.2393
100 V A 0.0000
101 F A 2.5092
102 G A 1.3240
103 G A 0.3035
104 G A -0.8605
105 T A 0.0000
106 K A -2.1962
107 L A 0.0000
108 T A -1.3288
109 V A -0.3118
110 L A 0.7940
111 G A 0.1416
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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, -0.5242 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 -0.5242 View CSV PDB
input -0.549 View CSV PDB
model_4 -0.5524 View CSV PDB
model_3 -0.573 View CSV PDB
model_0 -0.6044 View CSV PDB
model_5 -0.6849 View CSV PDB
model_11 -0.6868 View CSV PDB
model_8 -0.7142 View CSV PDB
model_10 -0.715 View CSV PDB
model_7 -0.7161 View CSV PDB
model_1 -0.7298 View CSV PDB
model_9 -0.7329 View CSV PDB
model_2 -0.74 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018