Aggrescan3D: SP2053TT [mutate: IT32A, IT38A]

Project name: SP2053TT [mutate: IT32A, IT38A]

Status: done

Started: 2020-02-14 15:50:33

Settings

Chain sequence(s)	A: FIDINDVIN input PDB
Selected Chain(s)	A
Distance of aggregation	10 Å
FoldX usage	Yes
Dynamic mode	Yes
Automated mutations	No
Mutated residues	IT32A,IT38A
Energy difference between WT (input) and mutated protein (by FoldX)	0.885068 kcal/mol
Downloads	Download all the data

Simulation log

Toggle log display

[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]       FoldX:    Building mutant model                                                       (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:05)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:07)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:02:08)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:02:09)
[INFO]       Movie:    Creting movie with webm format                                              (00:02:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:49)

Note Your prediction results will be deleted after 360 days.

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -1.1095
Maximal score value: 2.2767
Average score: 0.4523
Total score value: 4.0703

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
31	F	A	2.2767
32	T	A	1.2202	mutated: IT32A
33	D	A	0.8289
34	I	A	1.5638
35	N	A	-0.6104
36	D	A	-1.1095
37	V	A	0.9657
38	T	A	-0.0454	mutated: IT38A
39	N	A	-1.0197

3Dmol can be expensive computationally for big molecules. If you experience lag or delay click on the "Play the video" button instead.

Download PDB file

View in 3Dmol

Start animation

Play the video

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, 0.4523 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	0.4523	View	CSV	PDB
input	0.1487	View	CSV	PDB
model_11	-0.013	View	CSV	PDB
model_10	-0.0942	View	CSV	PDB
model_0	-0.1347	View	CSV	PDB
model_3	-0.1461	View	CSV	PDB
model_6	-0.1495	View	CSV	PDB
model_1	-0.1535	View	CSV	PDB
model_7	-0.1658	View	CSV	PDB
model_9	-0.1816	View	CSV	PDB
model_2	-0.2475	View	CSV	PDB
model_5	-0.2751	View	CSV	PDB
model_4	-0.4179	View	CSV	PDB

Project name: SP2053TT [mutate: IT32A, IT38A]

Status: done

Started: 2020-02-14 15:50:33

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score