Project name: d2ea3f2bd10e2

Status: done

Started: 2023-09-25 14:07:29
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                                                (00:00:11)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:29)
[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.                                          (00:02:30)
Show buried residues

Minimal score value
-2.1661
Maximal score value
3.6125
Average score
0.2554
Total score value
6.3847

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 0.1812
71 C A 0.3080
72 T A -0.0509
73 H A 0.0000
74 G A 1.5629
75 L A 2.7347
76 Y A 2.1665
77 K A -0.5762
78 R A -2.1661
79 T A -1.8615
80 P A -1.7092
81 R A -2.1617
82 Y A -0.2875
83 P A -0.8260
84 E A -1.9930
85 E A -1.5695
86 L A 0.4072
87 L A 2.3943
88 L A 3.5991
89 L A 3.6125
90 V A 2.8493
91 S A 0.7375
92 Q A -0.7732
93 C A 0.0627
94 S A -0.2564
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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, 0.2554 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_8 0.2554 View CSV PDB
model_1 0.1957 View CSV PDB
model_11 0.1808 View CSV PDB
model_3 0.1722 View CSV PDB
model_6 0.1394 View CSV PDB
model_4 0.1305 View CSV PDB
input 0.0969 View CSV PDB
model_9 0.0443 View CSV PDB
model_10 0.0226 View CSV PDB
model_0 -0.0209 View CSV PDB
model_2 -0.0654 View CSV PDB
model_7 -0.0833 View CSV PDB
model_5 -0.1146 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018