Workbench
General information
Name: NSP16 in aqueous solution
Included proteins: NSP16
Uniprot ID: P0DTD1
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6W4H
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: 108754
Simulation details
Software and version: AceMD 3.2.3
Forcefield and version: CHARMM36 2019
Time step : 4.0 fs
Delta : 0.4 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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Site of interest
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Toolkit
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:
Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.
| Substitution scores | ||
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| BLOSUM90 score | ||
| Δ charge | ||
| Epstein's coefficient of difference | ||
| Experimental exchangeability | ||
| Grantham's distance | ||
| Miyata's distance | ||
| Sneath's index | ||
| Δ hydrophobicity | ||
| Conservation | ||
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| Frequency (‰) | ||
| SIFT4G Score | ||
| SIFT4G Median IC | ||
| Structure | ||
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| Post-translational modification | ||
| Surface accessibility | ||
| FoldX ΔΔG | ||
| Experimental | ||
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| Mean Experimental Antibody Escape | ||
| Max. Experimental Antibody Escape | ||
| Others | ||
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| Annotation | ||
| Parameter | Average | Weight average | SD | Weight SD | |
| RMSD |
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| RMSF |
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| SASA |
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| CHI1 |
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| All contacts |
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| Hydrogen bond contacts |
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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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