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Simulation report and files

General information

Name: NendoU NSP15 in aqueous solution

Included proteins: NSP15

Uniprot ID: P0DTD1

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

PDB ID: 6VWW

Submitted by: Institut Hospital del Mar d'Investigacions Mèdiques

Submission date: March 04, 2021

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P

Total number of atoms: 88694

Simulation details

Software and version: AceMD 3.2.3

Forcefield and version: CHARMM36 2019

Time step : 4.0 fs

Delta : 0.2 ns

Replicates: 1

Accumulated simulation time: 1.0000 µs

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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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NendoU NSP15 in aqueous solution ( 6VWW)

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Interaction network

Hydrogen bonds

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RMSD
Trajectory:
Frames:
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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
NSP15
AA
Seq. pos.
PDB resID
S
1
2
L
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E
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N
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V
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6
A
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Q
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347
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

Please select a variant from the sequence above.
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

Upload your own descriptors according to this template.