Project name: 9ea2e1cc83d4fd5

Status: done

Started: 2023-09-25 12:59:09
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPEELELLVSQCS
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]                                                (00:00:01)
[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]       CABS:     Running CABS flex simulation                                                (00:00:11)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:34)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:34)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:35)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:36)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:36)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:36)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:36)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:36)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:36)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:37)
Show buried residues

Minimal score value
-2.9232
Maximal score value
3.216
Average score
-0.0508
Total score value
-1.2696

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 T A 0.1005
71 C A 0.2292
72 T A -0.2892
73 H A 0.1444
74 G A 1.7778
75 L A 2.4001
76 Y A 2.1307
77 K A -0.6836
78 R A -2.3534
79 T A -2.1803
80 P A -2.1792
81 R A -2.3919
82 Y A -0.4235
83 P A -1.3516
84 E A -2.9232
85 E A -2.4401
86 L A -0.0521
87 E A 0.6691
88 L A 2.8747
89 L A 3.2160
90 V A 2.4257
91 S A 0.6823
92 Q A -0.6221
93 C A 0.0978
94 S A -0.1277
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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, -0.0508 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_10 -0.0508 View CSV PDB
model_6 -0.1577 View CSV PDB
model_11 -0.2422 View CSV PDB
model_0 -0.2517 View CSV PDB
model_1 -0.3494 View CSV PDB
model_7 -0.3662 View CSV PDB
model_4 -0.3925 View CSV PDB
model_3 -0.3988 View CSV PDB
model_2 -0.4717 View CSV PDB
input -0.4952 View CSV PDB
model_9 -0.5231 View CSV PDB
model_5 -0.5631 View CSV PDB
model_8 -0.6739 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018