Aggrescan3D: 8888

Project name: 8888

Status: done

Started: 2021-10-18 15:16:20

Settings

Chain sequence(s)	A: CNINDINDINNVC 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

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[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:04)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:31)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:32)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:02:32)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:33)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:02:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:33)

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Show buried residues

Minimal score value: -1.4656
Maximal score value: 1.7173
Average score: -0.0361
Total score value: -0.4689

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
1	C	A	0.4341
2	N	A	-0.0129
3	I	A	1.0280
4	N	A	-0.3820
5	D	A	-1.2968
6	I	A	-0.0615
7	N	A	-1.3681
8	D	A	-1.4656
9	I	A	-0.0048
10	N	A	-0.5532
11	N	A	0.2136
12	V	A	1.7173
13	C	A	1.2830

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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, -0.0361 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_6	-0.0361	View	CSV	PDB
model_4	-0.0829	View	CSV	PDB
model_5	-0.1037	View	CSV	PDB
model_10	-0.1052	View	CSV	PDB
model_0	-0.1281	View	CSV	PDB
input	-0.2096	View	CSV	PDB
model_2	-0.2365	View	CSV	PDB
model_1	-0.2384	View	CSV	PDB
model_3	-0.3224	View	CSV	PDB
model_7	-0.3769	View	CSV	PDB
model_11	-0.4257	View	CSV	PDB
model_9	-0.7218	View	CSV	PDB
model_8	-0.763	View	CSV	PDB

Project name: 8888

Status: done

Started: 2021-10-18 15:16:20

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score