About: Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

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About: Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors 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	Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
Creator	Ae, Ae Ae, Eitner Ae, Rychlewski Ae, Szkoda Banachowicz, E Banachowicz, Ewa Eitner, Ae Hoffmann, M Hoffmann, Marcin Kolinski, A Kolinski, Andrzej Krystian, A Leszek, A Tomasz Grabarkiewicz, A Tomasz, A Von Grotthuss, Ae Von Grotthuss, Marcin
Source	Medline; PMC
abstract	The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.
has issue date	2006-09-14(xsd:dateTime)
bibo:doi	10.1007/s10822-006-9057-z
bibo:pmid	16972168
has license	no-cc
sha1sum (hex)	48bc36b582d9d13ef7f44b17181ac36007384d64
schema:url	https://doi.org/10.1007/s10822-006-9057-z
resource representing a document's title	Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
has PubMed Central identifier	PMC7088412
has PubMed identifier	16972168
schema:publication	J Comput Aided Mol Des
resource representing a document's body	covid:48bc36b582d9d13ef7f44b17181ac36007384d64#body_text
is schema:about of	named entity 'simulations' named entity '3D model' named entity 'possessing' named entity 'functional groups' named entity 'helicase' named entity 'ATPase' named entity 'sites' named entity 'acid' named entity 'moieties' named entity 'pocket' named entity 'ends' named entity 'distal' named entity 'severe acute respiratory syndrome coronavirus' named entity 'modeling' named entity 'catalytic' named entity 'interacted' named entity 'creating' named entity 'model selection' named entity 'This' named entity 'protein structure prediction' named entity 'Jury' named entity 'catalytic domain' named entity '3D model' named entity 'catalytic domain' named entity 'inhibit the enzymatic activity' named entity 'database' named entity 'pharmacophores' named entity 'molecular dynamics' named entity 'SARS CoV' named entity '3D-Jury' named entity 'catalytic domain' named entity 'small molecule' named entity 'virus replication' named entity 'experimental studies' named entity 'superfamily' named entity 'gene' named entity 'CSD' named entity 'positively charged' named entity 'ATP' named entity 'molecular interactions' named entity 'peptide' named entity 'molecular dynamics' named entity 'NH 2' named entity 'SARS CoV' named entity 'Secondary structure' named entity 'atom' named entity 'ATP' named entity 'NH 2' named entity 'moiety' named entity 'SARS CoV' named entity 'phosphate' named entity 'ligand' named entity 'root mean square' named entity 'protein interactions' named entity 'NTP' named entity 'protein' named entity 'force field' named entity 'ATP' named entity 'aqueous' named entity 'ATP' named entity 'AM1' named entity 'protein' named entity 'ligand' named entity 'SARS CoV' named entity 'ATP'

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