Project name: 616a49aa1ba077e

Status: done

Started: 2020-04-05 14:28:25
Settings
Chain sequence(s) A: NFMLTQPHSVSESPGKTLTISCTGSSASIASHYVQWYSIDSSSNSASLTISGLKTEDEADYYCQSYDGNNHWVFGGG
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                                                (00:00:23)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:11:30)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:11:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:11:30)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:11:31)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:11:32)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:11:32)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:11:32)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:11:32)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:11:33)
[INFO]       Movie:    Creting movie with webm format                                              (00:12:57)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:59)
Show buried residues
Minimal score value
-3.3067
Maximal score value
2.9278
Average score
-0.0807
Total score value
-6.2116
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 N A 0.0000
2 F A 0.0000
3 M A 0.0000
4 L A 0.0000
5 T A -0.1227
6 Q A 0.0000
7 P A 0.0521
8 H A -0.3088
9 S A 0.1616
10 V A 0.8972
11 S A -0.1112
12 E A -1.1834
13 S A 0.0000
14 P A -0.9297
15 G A 0.0000
16 K A -0.5757
17 T A 0.3510
18 L A 1.1920
19 T A 0.9861
20 I A 0.4200
21 S A 0.2593
22 C A 0.0000
23 T A 0.0000
24 G A 0.3437
25 S A 0.0293
26 S A 0.0000
27 A A 0.2227
28 S A 0.6124
29 I A 1.0807
30 A A 0.5007
31 S A 0.1780
32 H A 0.0647
33 Y A 0.0000
34 V A 0.0000
35 Q A 0.6656
36 W A 1.1110
37 Y A 1.0214
66 S A 0.0000
67 I A -0.1692
68 D A -1.4139
69 S A -1.1211
70 S A -1.0854
71 S A -0.8366
72 N A -0.5690
73 S A -0.1645
74 A A 0.3635
75 S A 0.4297
76 L A 1.3442
77 T A 1.1781
78 I A 1.4870
79 S A -0.0229
80 G A -0.8272
81 L A -1.2543
82 K A -2.4485
83 T A -1.9482
84 E A -2.2027
85 D A -3.3067
86 E A -3.1143
87 A A -1.4224
88 D A -0.5669
89 Y A 1.3477
90 Y A 2.2961
91 C A 2.3276
92 Q A 0.0000
93 S A 0.0609
94 Y A -0.3314
95 D A -2.0885
96 G A -1.8853
97 N A -1.4762
98 N A -1.1415
99 H A 0.3105
100 W A 2.0285
101 V A 2.9278
102 F A 1.8739
103 G A 0.2590
104 G A -0.9101
105 G A -1.0573
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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, -0.0807 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_11 -0.0807 View CSV PDB
input -0.0924 View CSV PDB
model_0 -0.1467 View CSV PDB
model_1 -0.1669 View CSV PDB
model_5 -0.2068 View CSV PDB
model_2 -0.2922 View CSV PDB
model_8 -0.3133 View CSV PDB
model_3 -0.317 View CSV PDB
model_4 -0.3172 View CSV PDB
model_10 -0.3277 View CSV PDB
model_7 -0.3318 View CSV PDB
model_6 -0.3572 View CSV PDB
model_9 -0.3756 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018