Project name: f8d711080997ccd

Status: done

Started: 2023-09-25 13:31:08
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPEELLLLVSQCS
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                                                (00:00:10)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:30)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:30)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:30)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:31)
Show buried residues

Minimal score value
-1.6711
Maximal score value
3.1474
Average score
0.3423
Total score value
8.5584

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 -0.0610
71 C A 0.2634
72 T A -0.0273
73 H A 0.1051
74 G A 1.4260
75 L A 2.3029
76 Y A 2.4805
77 K A 0.2273
78 R A -1.4421
79 T A -1.1822
80 P A -1.3820
81 R A -1.6711
82 Y A -0.5061
83 P A -1.0254
84 E A -1.3984
85 E A -1.2810
86 L A 1.1263
87 L A 2.4001
88 L A 3.1474
89 L A 3.0530
90 V A 2.4650
91 S A 0.5915
92 Q A -0.6620
93 C A -0.1284
94 S A -0.2631
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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, 0.3423 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 0.3423 View CSV PDB
model_5 0.2346 View CSV PDB
model_7 0.0989 View CSV PDB
input 0.0969 View CSV PDB
model_3 0.0698 View CSV PDB
model_9 0.0658 View CSV PDB
model_2 0.0531 View CSV PDB
model_8 0.0465 View CSV PDB
model_0 0.0347 View CSV PDB
model_4 0.0323 View CSV PDB
model_6 0.0108 View CSV PDB
model_10 -0.1245 View CSV PDB
model_1 -0.1503 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018