Project name: 667c0b75ff8cc61 [mutate: VT85A]

Status: done

Started: 2023-09-25 13:19:50
Settings
Chain sequence(s) A: PSTHVKLTHTISRIAVSYQTPVNLKSAIRSPCQ
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues VT85A
Energy difference between WT (input) and mutated protein (by FoldX) -0.0480043 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:00:07)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:07)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:14)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:03:04)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:03:05)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:03:05)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:05)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:03:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:06)
Show buried residues
Minimal score value
-1.0985
Maximal score value
1.3369
Average score
-0.0251
Total score value
-0.8297
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
70 P A -0.8425
71 S A -0.7052
72 T A -0.7578
73 H A -0.9064
74 V A -0.1691
75 K A -0.9437
76 L A 0.1657
77 T A -0.0119
78 H A -0.5424
79 T A 0.1199
80 I A 1.2558
81 S A 0.4325
82 R A 0.1097
83 I A 1.3369
84 A A 0.4133
85 T A 0.1441 mutated: VT85A
86 S A 0.3192
87 Y A 0.8174
88 Q A -0.0563
89 T A 0.3245
90 P A 0.5647
91 V A 1.0880
92 N A 0.0664
93 L A 0.6496
94 K A -0.7327
95 S A -0.3716
96 A A 0.2974
97 I A 0.5374
98 R A -0.8491
99 S A -0.5610
100 P A -0.3777
101 C A -0.5463
102 Q A -1.0985
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, -0.0251 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_0 -0.0251 View CSV PDB
model_9 -0.1036 View CSV PDB
model_7 -0.1349 View CSV PDB
model_11 -0.144 View CSV PDB
model_8 -0.1778 View CSV PDB
model_4 -0.2139 View CSV PDB
model_3 -0.2605 View CSV PDB
model_6 -0.2912 View CSV PDB
model_2 -0.3468 View CSV PDB
model_5 -0.381 View CSV PDB
model_10 -0.3822 View CSV PDB
model_1 -0.4239 View CSV PDB
input -0.4454 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018