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Simulation report and files

General information

Name: SARS-CoV-2 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

Extracted from: BioExcel (ID: MCV1900006)

Author: Vito Genna

Submission date: October 22, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 2985

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

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

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SARS-CoV-2 spike receptor binding domain ( 6VW1)

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Toolkit

General
Interaction network

Hydrogen bonds

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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(K)
346
13
F
347
14
A(P)
348
15
S
349
16
V
350
17
Y
351
18
A
352
19
W
353
20
N(E)
354
21
R
355
22
K
356
23
R(K)
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(F)
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(A)
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(S)
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(V)
402
69
R(K)
403
70
G
404
71
D
405
72
E(D)
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(V)
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(M)
430
97
G
431
98
C
432
99
V
433
100
I(L)
434
101
A
435
102
W
436
103
N
437
104
S(T)
438
105
N(R)
439
106
N
440
107
L(I)
441
108
D
442
109
S
443
112
G(T)
446
113
G
447
114
N
448
115
Y
449
116
N
450
117
Y
451
118
L(K)
452
119
Y
453
120
R
454
121
L
455
122
F
456
123
R
457
124
K
458
125
S
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
478
145
P
479
146
C
480
147
N
481
148
G
482
149
V
483
150
E
484
151
G
485
152
F
486
153
N
487
154
C
488
155
Y
489
156
F
490
157
P
491
158
L
492
159
Q
493
160
S
494
161
Y
495
162
G
496
163
F
497
164
Q
498
165
P
499
166
T
500
167
N
501
168
G
502
169
V
503
170
G
504
171
Y
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
189
V
524
190
C
525
191
G
526
192
P
527
193
Impact score

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

Mutation effect 0/16
Substitution scores
0
 BLOSUM90 score
0
 Δ charge
0
 Epstein's coefficient of difference
0
 Experimental exchangeability
0
 Grantham's distance
0
 Miyata's distance
0
 Sneath's index
0
 Δ hydrophobicity
Conservation
0
 Frequency (‰)
0
 SIFT4G Score
0
 SIFT4G Median IC
Structure
0
 Post-translational modification
0
 Surface accessibility
0
 FoldX ΔΔG
Experimental
0
 Mean Experimental Antibody Escape
0
 Max. Experimental Antibody Escape
Others
Annotation
Time-dependent 0/28
Parameter Average Weight average SD Weight SD
RMSD
0
0

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RMSF
0
0

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SASA
0
0

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CHI1
0
0

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All contacts
0
0

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Hydrogen bond contacts
0
0

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Salt bridge contacts
0
0

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Hydrophobic contacts
0
0

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Pi-cation contacts
0
0

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Pi-stacking contacts
0
0

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T-stacking contacts
0
0

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Van der Waals contacts
0
0

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Water bridge contacts
0
0

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Extended water bridge contacts
0
0

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User-provided descriptors 0/0

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