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Simulation report and files

General information

Name: Bat-SARSr-CoV RATG13 spike receptor binding domain bound with PUS ACE2

Included proteins: Spike, ACE2

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: MCV1900017)

Author: Vito Genna

Submission date: October 22, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 12589

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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Bat-SARSr-CoV RATG13 spike receptor binding domain bound with PUS ACE2 ( 6VW1)

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Toolkit

General
Interaction network

Hydrogen bonds

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RMSD
Trajectory:
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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
600
L
335
601
C
336
602
P
337
603
F
338
604
G
339
605
E
340
606
V
341
607
F
342
608
N
343
609
A
344
610
T
345
611
R(T)
346
612
F
347
613
A
348
614
S
349
615
V
350
616
Y
351
617
A
352
618
W
353
619
N
354
620
R
355
621
K
356
622
R
357
623
I
358
624
S
359
625
N
360
626
C
361
627
V
362
628
A
363
629
D
364
630
Y
365
631
S
366
632
V
367
633
L
368
634
Y
369
635
N
370
636
S
371
637
A(T)
372
638
S
373
639
F
374
640
S
375
641
T
376
642
F
377
643
K
378
644
C
379
645
Y
380
646
G
381
647
V
382
648
S
383
649
P
384
650
T
385
651
K
386
652
L
387
653
N
388
654
D
389
655
L
390
656
C
391
657
F
392
658
T
393
659
N
394
660
V
395
661
Y
396
662
A
397
663
D
398
664
S
399
665
F
400
666
V
401
667
I
402
668
R(T)
403
669
G
404
670
D
405
671
E
406
672
V
407
673
R
408
674
Q
409
675
I
410
676
A
411
677
P
412
678
G
413
679
Q
414
680
T
415
681
G
416
682
K
417
683
I
418
684
A
419
685
D
420
686
Y
421
687
N
422
688
Y
423
689
K
424
690
L
425
691
P
426
692
D
427
693
D
428
694
F
429
695
T
430
696
G
431
697
C
432
698
V
433
699
I
434
700
A
435
701
W
436
702
N
437
703
S
438
704
N(K)
439
705
N(H)
440
706
L(I)
441
707
D
442
708
S(E)
443
711
G
446
712
G
447
713
N
448
714
Y(F)
449
715
N
450
716
Y
451
717
L
452
718
Y
453
719
R
454
720
L
455
721
F
456
722
R
457
723
K
458
724
S(A)
459
725
N
460
726
L
461
727
K
462
728
P
463
729
F
464
730
E
465
731
R
466
732
D
467
733
I
468
734
S
469
735
T
470
736
E
471
737
I
472
738
Y
473
739
Q
474
740
A
475
741
G
476
742
S
477
743
T(K)
478
744
P
479
745
C
480
746
N
481
747
G
482
748
V(Q)
483
749
E(T)
484
750
G
485
751
F(L)
486
752
N
487
753
C
488
754
Y
489
755
F(Y)
490
756
P
491
757
L
492
758
Q(Y)
493
759
S(R)
494
760
Y
495
761
G
496
762
F
497
763
Q(Y)
498
764
P
499
765
T
500
766
N(D)
501
767
G
502
768
V
503
769
G
504
770
Y(H)
505
771
Q
506
772
P
507
773
Y
508
774
R
509
775
V
510
776
V
511
777
V
512
778
L
513
779
S
514
780
F
515
781
E
516
782
L
517
783
L
518
784
H(N)
519
785
A
520
786
P
521
787
T
523
789
V
524
790
C
525
791
G
526
792
P
527
793
Impact score

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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
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Hydrophobic contacts
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Pi-cation contacts
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Pi-stacking contacts
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T-stacking contacts
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Van der Waals contacts
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Water bridge contacts
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Extended water bridge contacts
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User-provided descriptors 0/0

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