Aggrescan3D: 1eb46f6472238e4

Project name: 1eb46f6472238e4

Status: done

Started: 2020-06-26 10:07:07

Settings

Chain sequence(s)	A: SAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEE P: QPPVPPQRPM input PDB
Selected Chain(s)	A,P
Distance of aggregation	10 Å
FoldX usage	Yes
Dynamic mode	Yes
Automated mutations	No
Downloads	Download all the data

Simulation log

Toggle log display

[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:04)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:04)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:04)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:04)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:39)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:19:14)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:19:16)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:19:16)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:19:17)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:19:17)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:19:17)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:19:19)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:19:26)
[INFO]       Movie:    Creting movie with webm format                                              (00:22:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:59)

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: -3.4504
Maximal score value: 0.6871
Average score: -1.1545
Total score value: -75.0439

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
5	S	A	-1.0820
6	A	A	-1.0733
7	V	A	0.0000
8	K	A	-1.5047
9	A	A	0.0000
10	L	A	0.6871
11	F	A	0.6784
12	D	A	-1.5968
13	Y	A	0.0000
14	K	A	-2.1014
15	A	A	-2.1771
16	Q	A	0.0000
17	R	A	-3.4504
18	E	A	-3.3698
19	D	A	-2.5927
20	E	A	-2.4484
21	L	A	0.0000
22	T	A	-0.5866
23	F	A	-0.5222
24	T	A	-0.9747
25	K	A	-1.4781
26	S	A	-0.3950
27	A	A	0.0000
28	I	A	0.3008
29	I	A	0.0000
30	Q	A	-1.2088
31	N	A	-1.6523
32	V	A	-1.4629
33	E	A	-2.1983
34	K	A	-2.8975
35	Q	A	-2.7509
36	D	A	-2.5989
37	G	A	-1.7445
38	G	A	-1.5549
39	W	A	0.0000
40	W	A	-1.5923
41	R	A	-1.4886
42	G	A	0.0000
43	D	A	-1.5327
44	Y	A	-0.2848
45	G	A	-1.0531
46	G	A	-1.7908
47	K	A	-2.7556
48	K	A	-3.0183
49	Q	A	-1.9237
50	L	A	0.0000
51	W	A	-0.9525
52	F	A	0.0000
53	P	A	0.0000
54	S	A	-1.3870
55	N	A	-1.4248
56	Y	A	0.0000
57	V	A	-1.0662
58	E	A	-2.7570
59	E	A	-2.7411
1	Q	P	-1.7173
2	P	P	-0.9298
3	P	P	-0.6272
4	V	P	-0.3947
5	P	P	-1.0655
6	P	P	-0.8174
7	Q	P	-1.1155
8	R	P	-1.1452
9	P	P	-0.3227
10	M	P	0.6158

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, -1.1545 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_4	-1.1545	View	CSV	PDB
model_9	-1.231	View	CSV	PDB
model_8	-1.2322	View	CSV	PDB
model_6	-1.2461	View	CSV	PDB
model_3	-1.2465	View	CSV	PDB
model_1	-1.2541	View	CSV	PDB
model_2	-1.2613	View	CSV	PDB
model_7	-1.2951	View	CSV	PDB
model_0	-1.2957	View	CSV	PDB
model_5	-1.3117	View	CSV	PDB
input	-1.3254	View	CSV	PDB
model_11	-1.3392	View	CSV	PDB
model_10	-1.4573	View	CSV	PDB

Project name: 1eb46f6472238e4

Status: done

Started: 2020-06-26 10:07:07

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score