Aggrescan3D: ORF7a

Project name: ORF7a

Status: done

Started: 2020-06-22 22:41:23

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Chain sequence(s)	A: ELYHYQECVRGTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARS 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                                                (00:01:14)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:15:11)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:15:11)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:15:11)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:15:12)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:15:12)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:15:12)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:15:13)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:15:13)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:15:13)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:15:14)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:15:14)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:15:14)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:15:15)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:15:20)
[INFO]       Movie:    Creting movie with webm format                                              (00:18:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:56)

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Show buried residues

Minimal score value: -2.4341
Maximal score value: 1.0297
Average score: -0.58
Total score value: -38.277

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	E	A	-1.5939
2	L	A	0.3284
3	Y	A	1.0094
4	H	A	0.3703
5	Y	A	0.4680
6	Q	A	-0.3171
7	E	A	-2.0210
8	C	A	0.0000
9	V	A	-0.6036
10	R	A	-1.7914
11	G	A	-1.2313
12	T	A	-0.8805
13	T	A	0.0587
14	V	A	0.6805
15	L	A	1.0297
16	L	A	-0.3264
17	K	A	-2.0523
18	E	A	0.0000
19	P	A	-0.8673
20	C	A	-0.7160
21	S	A	-0.4437
22	S	A	-0.5999
23	G	A	-0.4036
24	T	A	-0.0295
25	Y	A	0.5947
26	E	A	-0.9289
27	G	A	-0.8347
28	N	A	-0.4158
29	S	A	0.0193
30	P	A	0.0000
31	F	A	0.7021
32	H	A	-0.4156
33	P	A	0.0000
34	L	A	0.5496
35	A	A	-0.4292
36	D	A	-2.0859
37	N	A	-1.8984
38	K	A	-1.9176
39	F	A	0.0000
40	A	A	0.1395
41	L	A	0.0000
42	T	A	0.5690
43	C	A	0.0000
44	F	A	0.6732
45	S	A	-0.6001
46	T	A	-0.4163
47	Q	A	-0.8949
48	F	A	0.0000
49	A	A	-0.3612
50	F	A	0.0000
51	A	A	-1.0332
52	C	A	-1.0406
53	P	A	-1.5679
54	D	A	-2.2694
55	G	A	-2.0286
56	V	A	-1.4972
57	K	A	-2.1573
58	H	A	0.0000
59	V	A	0.1038
60	Y	A	0.0000
61	Q	A	-0.6342
62	L	A	0.0000
63	R	A	-2.3486
64	A	A	-1.8318
65	R	A	-2.4341
66	S	A	-1.6542

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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, -0.58 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	-0.58	View	CSV	PDB
model_8	-0.5806	View	CSV	PDB
model_10	-0.7002	View	CSV	PDB
model_11	-0.7231	View	CSV	PDB
model_0	-0.7415	View	CSV	PDB
model_9	-0.787	View	CSV	PDB
model_1	-0.816	View	CSV	PDB
model_2	-0.8518	View	CSV	PDB
model_5	-0.8549	View	CSV	PDB
model_7	-0.9039	View	CSV	PDB
input	-0.9051	View	CSV	PDB
model_4	-0.977	View	CSV	PDB
model_3	-1.0182	View	CSV	PDB

Project name: ORF7a

Status: done

Started: 2020-06-22 22:41:23

CABS-flex predictions of flexibility of input structure

Model

Average A3D Score