About: Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

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About: Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane
Creator	Cao, Yiwei Croll, Tristan Im, Wonpil Kern, Nathan Lee, Jumin Park, Sang-Jun Park, Taeyong Seok, Chaok Tanveer, Maham Woo, Hyeonuk Yeom, Min Choi, Yeol
Source	BioRxiv; Medline; PMC
abstract	This technical study describes all-atom modeling and simulation of a fully-glycosylated full-length SARS-CoV-2 spike (S) protein in a viral membrane. First, starting from PDB:6VSB and 6VXX, full-length S protein structures were modeled using template-based modeling, de-novo protein structure prediction, and loop modeling techniques in GALAXY modeling suite. Then, using the recently-determined most occupied glycoforms, 22 N-glycans and 1 O-glycan of each monomer were modeled using Glycan Reader & Modeler in CHARMM-GUI. These fully-glycosylated full-length S protein model structures were assessed and further refined against the low-resolution data in their respective experimental maps using ISOLDE. We then used CHARMM-GUI Membrane Builder to place the S proteins in a viral membrane and performed all-atom molecular dynamics simulations. All structures are available in CHARMM-GUI COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19), so researchers can use these models to carry out innovative and novel modeling and simulation research for the prevention and treatment of COVID-19.
has issue date	2020-05-21(xsd:dateTime)
bibo:doi	10.1101/2020.05.20.103325
bibo:pmid	32511389
has license	no-cc
sha1sum (hex)	248a7c630316284f035a02ce1c0b1909a3d5deb2
schema:url	https://doi.org/10.1101/2020.05.20.103325
resource representing a document's title	Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane
has PubMed Central identifier	PMC7263518
has PubMed identifier	32511389
schema:publication	bioRxiv
resource representing a document's body	covid:248a7c630316284f035a02ce1c0b1909a3d5deb2#body_text
is schema:about of	named entity 'http' named entity 'protein structure prediction' named entity 'COVID-19' named entity 'Membrane' named entity 'Builder' named entity 'Reader' named entity 'PDB' named entity 'simulation' named entity 'structures' named entity 'protein' named entity 'prevention' named entity 'SARS-CoV-2' named entity 'starting' named entity 'atom' named entity 'ISOLDE' named entity 'Glycan' named entity 'glycosylated' named entity 'CHARMM' named entity 'viral membrane' named entity 'glycosylated' named entity 'biomolecules' named entity 'CHARMM' named entity 'GlcNAc' named entity 'triage' named entity 'genetic mutations' named entity 'C-terminal' named entity 'secondary structure prediction' named entity 'ab initio' named entity 'glycans' named entity 'docking module' named entity 'Cys' named entity 'virus' named entity 'glycan' named entity 'helical' named entity 'glycosylation' named entity 'GROMACS' named entity 'NVT' named entity 'glycosylated' named entity 'glycosylated' named entity 'GlcNAc' named entity 'secondary structure' named entity 'GlcNAc' named entity 'ring structures' named entity 'protein structure' named entity 'Loop modeling' named entity 'S protein' named entity 'B-factor' named entity 'GUI' named entity 'lipid' named entity 'lipid' named entity 'monomer' named entity 'RBD' named entity 'HR2' named entity 'long time' named entity 'SARS-CoV-1' named entity 'CHARMM' named entity 'gp-41' named entity 'loop modeling' named entity 'N-glycosylated' named entity 'N-linked glycans' named entity 'protein' named entity 'S protein' named entity 'sterols' named entity 'glycosylated' named entity 'SARS-CoV-1' named entity 'PDB' named entity 'loop modeling' named entity 'Glycan' named entity 'protein' named entity 'random coil'

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