Aggrescan3D: 0023

Project name: 0023

Status: done

Started: 2021-10-13 20:30:29

Settings

Chain sequence(s)	A: FIDINDVINFASQNDYSYWL 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]                                                (00:00:01)
[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                                                (00:00:06)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:03:47)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:03:48)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:03:48)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:03:49)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:03:49)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:03:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:50)

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Show buried residues

Minimal score value: -1.759
Maximal score value: 3.3778
Average score: 0.937
Total score value: 18.7402

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	F	A	2.8227
2	I	A	3.3778
3	D	A	1.1250
4	I	A	1.9579
5	N	A	0.1619
6	D	A	-0.9379
7	V	A	1.1451
8	I	A	1.4768
9	N	A	0.3753
10	F	A	1.3196
11	A	A	0.0893
12	S	A	-0.9087
13	Q	A	-1.6933
14	N	A	-1.7590
15	D	A	-0.6211
16	Y	A	1.4826
17	S	A	1.8652
18	Y	A	2.6026
19	W	A	2.6156
20	L	A	2.2428

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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, 0.937 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_2	0.937	View	CSV	PDB
model_7	0.8084	View	CSV	PDB
model_4	0.7835	View	CSV	PDB
model_1	0.7575	View	CSV	PDB
model_9	0.6327	View	CSV	PDB
input	0.6003	View	CSV	PDB
model_6	0.5517	View	CSV	PDB
model_10	0.5307	View	CSV	PDB
model_0	0.4581	View	CSV	PDB
model_3	0.4265	View	CSV	PDB
model_5	0.3267	View	CSV	PDB
model_8	0.2856	View	CSV	PDB
model_11	0.2733	View	CSV	PDB

Project name: 0023

Status: done

Started: 2021-10-13 20:30:29

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score