Project name: 43c60430d953a9

Status: done

Started: 2023-09-25 13:48:57
Settings
Chain sequence(s) A: TCTHGLYKRTPRYPELLELLVSQCS
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                                                (00:00:12)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:30)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:31)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:31)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:32)
Show buried residues

Minimal score value
-1.8223
Maximal score value
3.3301
Average score
0.4689
Total score value
11.7225

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 0.2188
71 C A 0.5058
72 T A 0.0245
73 H A -0.2077
74 G A 1.2576
75 L A 2.4320
76 Y A 2.5966
77 K A 0.1089
78 R A -1.6094
79 T A -1.2056
80 P A -1.5031
81 R A -1.8223
82 Y A -0.1131
83 P A -0.5680
84 E A -1.4844
85 L A 0.5837
86 L A 1.4699
87 E A 1.4251
88 L A 3.3251
89 L A 3.3301
90 V A 2.7286
91 S A 0.7198
92 Q A -0.5366
93 C A 0.1577
94 S A -0.1115
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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, 0.4689 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 0.4689 View CSV PDB
model_7 0.2181 View CSV PDB
model_3 0.2147 View CSV PDB
model_11 0.1126 View CSV PDB
model_6 0.0945 View CSV PDB
model_8 0.0454 View CSV PDB
model_4 0.0358 View CSV PDB
model_9 0.0323 View CSV PDB
input -0.0367 View CSV PDB
model_1 -0.0464 View CSV PDB
model_2 -0.0559 View CSV PDB
model_10 -0.2277 View CSV PDB
model_5 -0.2424 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018