Free cookie consent management tool by TermsFeed SCoV2-MD

Workbench

Simulation report and files

General information

Name: Bat-SARSr-CoV RATG13 spike receptor binding domain

Included proteins: Spike

Uniprot ID: P0DTC2

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6VW1

Description: Theoretical model generated using Modeller from the PDB 6vw1

Extracted from: BioExcel (ID: MCV1900003)

Author: Vito Genna

Submission date: October 22, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 3004

Simulation details

Software and version: GROMACS 2019.1

Time step : 2.0 fs

Delta : 0.1 ns

Replicates: 1

Accumulated simulation time: 0.2001 µs



References

SARS-CoV-2 Inhibition, Host Selection and Next-Move Prediction Through High-Performance Computing. Vito Genna1, Adam Hospital1 and Modesto Orozco1,2
1. Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology,C/ Baldiri Reixac 10-12, Barcelona 08028, Spain
2. Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona 08028, Spain


Visualization and trajectory sharing powered by NGL Viewer and MDsrv.

The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

Viewer

Bat-SARSr-CoV RATG13 spike receptor binding domain ( 6VW1)

Selection

Quick selection
Relevant domains

Region of interest

Domain of interest

Custom selection
Input your selection using the NGL selection language.

Toolkit

General
Interaction network

Hydrogen bonds

RMSD
Trajectory:
Frames:
All
From to
Stride:
Reference: frame from trajectory
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
RMSF
Trajectory:
Frames:
All
From to
Stride:
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact

Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:

Display isolate: All isolates
Spike
AA
Seq. pos.
PDB resID
N
334
1
L
335
2
C
336
3
P
337
4
F
338
5
G
339
6
E
340
7
V
341
8
F
342
9
N
343
10
A
344
11
T
345
12
R(T)
346
13
F
347
14
A
348
15
S
349
16
V
350
17
Y
351
18
A
352
19
W
353
20
N
354
21
R
355
22
K
356
23
R
357
24
I
358
25
S
359
26
N
360
27
C
361
28
V
362
29
A
363
30
D
364
31
Y
365
32
S
366
33
V
367
34
L
368
35
Y
369
36
N
370
37
S
371
38
A(T)
372
39
S
373
40
F
374
41
S
375
42
T
376
43
F
377
44
K
378
45
C
379
46
Y
380
47
G
381
48
V
382
49
S
383
50
P
384
51
T
385
52
K
386
53
L
387
54
N
388
55
D
389
56
L
390
57
C
391
58
F
392
59
T
393
60
N
394
61
V
395
62
Y
396
63
A
397
64
D
398
65
S
399
66
F
400
67
V
401
68
I
402
69
R(T)
403
70
G
404
71
D
405
72
E
406
73
V
407
74
R
408
75
Q
409
76
I
410
77
A
411
78
P
412
79
G
413
80
Q
414
81
T
415
82
G
416
83
K
417
84
I
418
85
A
419
86
D
420
87
Y
421
88
N
422
89
Y
423
90
K
424
91
L
425
92
P
426
93
D
427
94
D
428
95
F
429
96
T
430
97
G
431
98
C
432
99
V
433
100
I
434
101
A
435
102
W
436
103
N
437
104
S
438
105
N(K)
439
106
N(H)
440
107
L(I)
441
108
D
442
109
S(E)
443
112
G
446
113
G
447
114
N
448
115
Y(F)
449
116
N
450
117
Y
451
118
L
452
119
Y
453
120
R
454
121
L
455
122
F
456
123
R
457
124
K
458
125
S(A)
459
126
N
460
127
L
461
128
K
462
129
P
463
130
F
464
131
E
465
132
R
466
133
D
467
134
I
468
135
S
469
136
T
470
137
E
471
138
I
472
139
Y
473
140
Q
474
141
A
475
142
G
476
143
S
477
144
T(K)
478
145
P
479
146
C
480
147
N
481
148
G
482
149
V(Q)
483
150
E(T)
484
151
G
485
152
F(L)
486
153
N
487
154
C
488
155
Y
489
156
F(Y)
490
157
P
491
158
L
492
159
Q(Y)
493
160
S(R)
494
161
Y
495
162
G
496
163
F
497
164
Q(Y)
498
165
P
499
166
T
500
167
N(D)
501
168
G
502
169
V
503
170
G
504
171
Y(H)
505
172
Q
506
173
P
507
174
Y
508
175
R
509
176
V
510
177
V
511
178
V
512
179
L
513
180
S
514
181
F
515
182
E
516
183
L
517
184
L
518
185
H(N)
519
186
A
520
187
P
521
188
T
523
190
V
524
191
C
525
192
G
526
193
P
527
194
Impact score

Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.