Project name: 5b4166d893f7b75

Status: done

Started: 2020-04-05 14:28:23
Settings
Chain sequence(s) A: GQRVTISCSGRSSNIGRNLVKWYQQFPGTAPKLLIYSNDQRPSGVPDRFSGSKSGTSASLAVSGLQSEDEADYYCAAWDATLNAWVFGGGT
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                                                (00:00:34)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:12:39)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:12:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:12:39)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:12:40)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:12:40)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:12:40)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:12:40)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:12:41)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:12:41)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:12:41)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:12:41)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:12:42)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:12:42)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:12:43)
[INFO]       Movie:    Creting movie with webm format                                              (00:14:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:14:17)
Show buried residues
Minimal score value
-2.9417
Maximal score value
2.6776
Average score
-0.0318
Total score value
-2.8917
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
15 G A -1.1967
16 Q A -1.5159
17 R A -2.2281
18 V A -0.7078
19 T A -0.5180
20 I A 0.4075
21 S A 0.2816
22 C A 0.7099
23 S A 0.2717
24 G A -0.0408
25 R A -0.5008
26 S A 0.3126
27 S A 0.0215
28 N A 0.0000
29 I A 1.8723
30 G A 1.0036
31 R A 0.5909
32 N A -0.1678
33 L A 1.4882
34 V A 2.0406
35 K A 0.4227
36 W A 0.7360
37 Y A 1.1509
38 Q A 0.1423
39 Q A -0.5449
40 F A -0.1918
41 P A -0.8691
42 G A -0.9353
43 T A -0.8811
44 A A -0.7670
45 P A 0.0000
46 K A -0.4682
47 L A 1.6554
48 L A 0.0000
49 I A 2.6336
50 Y A 0.8877
51 S A -0.4009
52 N A -1.8055
53 D A -2.1146
54 Q A -2.1810
55 R A -1.4450
56 P A -0.6869
57 S A -0.2103
58 G A 0.0000
59 V A 0.0000
60 P A 0.0000
61 D A -2.4587
62 R A -2.9417
63 F A 0.0000
64 S A -1.4452
65 G A 0.0000
66 S A -1.2060
67 K A -1.9981
68 S A 0.0000
69 G A -1.4939
70 T A -1.2940
71 S A -1.0036
72 A A -0.0492
73 S A 0.3468
74 L A 2.1469
75 A A 0.0000
76 V A 0.6662
77 S A 0.0439
78 G A 0.0000
79 L A 0.8576
80 Q A 0.0000
81 S A -0.7429
82 E A 0.0000
83 D A -1.3509
84 E A 0.0000
85 A A -0.2870
86 D A 0.3530
87 Y A 1.3208
88 Y A 1.7328
89 C A 1.1146
90 A A 0.6741
91 A A 0.6423
92 W A 0.8383
93 D A -0.7481
94 A A 0.0000
95 T A -0.4935
96 L A 0.7490
97 N A -0.5757
98 A A 0.8566
99 W A 1.8756
100 V A 2.6776
101 F A 2.5656
102 G A 0.7491
103 G A -0.0071
104 G A -0.6003
105 T A -0.6581
Download PDB file
View in 3Dmol
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, -0.0318 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_4 -0.0318 View CSV PDB
model_2 -0.0554 View CSV PDB
model_11 -0.0756 View CSV PDB
model_6 -0.1063 View CSV PDB
model_7 -0.1279 View CSV PDB
model_1 -0.1682 View CSV PDB
model_0 -0.1778 View CSV PDB
input -0.2315 View CSV PDB
model_10 -0.2836 View CSV PDB
model_3 -0.3367 View CSV PDB
model_8 -0.3498 View CSV PDB
model_5 -0.3901 View CSV PDB
model_9 -0.4599 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018