About: Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

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About: Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model 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	Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
Creator	Cao, Yiwei Choi, Kyo Croll, Tristan Im, Wonpil Kern, Nathan Lee, Jumin Park, Sang-Jun Park, Taeyong Seok, Chaok Tanveer, Maham Woo, Hyeonuk Yeol, ¶ Yeom, Min
topic	covid:67c29da765ce7a75a7002a53d5d3037dba380a13#this
Source	Medline; PMC
abstract	[Image: see text] 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 that 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	2020-06-19(xsd:dateTime)
bibo:doi	10.1021/acs.jpcb.0c04553
bibo:pmid	32559081
has license	no-cc
sha1sum (hex)	67c29da765ce7a75a7002a53d5d3037dba380a13
schema:url	https://doi.org/10.1021/acs.jpcb.0c04553
resource representing a document's title	Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane
has PubMed Central identifier	PMC7341691
has PubMed identifier	32559081
schema:publication	J Phys Chem B
resource representing a document's body	covid:67c29da765ce7a75a7002a53d5d3037dba380a13#body_text
is http://vocab.deri.ie/void#inDataset of	https://covidontheweb.inria.fr:4443/about/id/http/ns.inria.fr/covid19/67c29da765ce7a75a7002a53d5d3037dba380a13
is schema:about of	named entity 'structures' named entity 'simulation' named entity 'researchers' named entity 'protein' named entity 'suite' named entity 'SPIKE' named entity 'EXPERIMENTAL' named entity 'TO PLACE' named entity 'TECHNICAL' named entity 'MAPS' named entity 'GALAXY' named entity 'ALL-ATOM MOLECULAR DYNAMICS SIMULATIONS' named entity 'USED' named entity 'GLYCOSYLATED' named entity 'LOOP' named entity 'STARTING' named entity 'protein' named entity 'Membrane' named entity 'glycosylated' named entity 'Reader' named entity 'study' named entity 'simulation' named entity 'molecular dynamics' named entity 'viral membrane' named entity 'docs' named entity 'ISOLDE' named entity 'viral membrane' named entity 'glycosylated' named entity 'COVID-19' named entity 'glycosylated' named entity 'O-glycan' named entity 'atom' named entity 'GUI' named entity 'protein structure prediction' named entity 'ISOLDE' named entity 'lipid' named entity 'viral envelope' named entity 'PSIPRED' named entity 'O-linked glycosylation' named entity 'neuraminic acid' named entity 'OpenMM' named entity 'ion' named entity 'SARS-CoV-1' named entity 'glycosylated' named entity 'lipid' named entity 'monomer' named entity 'carbohydrates' named entity 'secondary structure' named entity 'NPT' named entity 'palmitoylation' named entity 'palmitoylated' named entity 'glycans' named entity 'glycans' named entity 'palmitoylation' named entity 'signal peptide' named entity 'CHARMM' named entity 'GUI' named entity 'atom' named entity 'receptor binding domain' named entity 'glycan' named entity 'glycosylated' named entity 'palmitoylation' named entity 'double bonds' named entity 'galactose' named entity 'protein' named entity 'viral membrane' named entity 'protein'

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