Protein-sol pKa: prediction of electrostatic frustration, with application to coronavirusesApplications Notes Published on 2020-10-152022-10-28 Journal: Bioinformatics [Category] Coronavirus, [키워드] acidic pH Alter ambient conformational conformations conserved coronavirus coronavirus spike protein coronavirus spike proteins demonstrated electrostatic endosomal pH group groups histidine implementation Influenza virus Intensive motivation murine hepatitis virus predicted protonation state residues Result solvent variant [DOI] 10.1093/bioinformatics/btaa646 PMC 바로가기 [Article Type] Applications Notes
Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2)Bioinformatics Published on 2020-09-292022-10-28 Journal: PeerJ [Category] COVID-19, [키워드] antigenic antigenicity antiviral drugs B cell B cell epitope B-cell binding binding interaction bioinformatics caused CD8 CD8+ T cell Cluster computational approach computational tools conformational Coverage COVID-19 directive Discovery Studio docking study effective epitope Epitopes FIVE greater identify Immune Epitope Database indicated Interaction lack linear linear B-cell epitope linear B-cell epitopes linear epitope majority membrane membrane protein nucleocapsid nucleocapsid protein Nucleocapsid proteins ORF3a ORF3a protein pandemic parameter peptide peptide epitopes peptide-based performed Perspective predicted produced required Result RNA virus robust SARS-CoV-2 Seven single-stranded positive-sense solvent structural protein Structure Surface glycoprotein T cell T cell epitope T cell epitopes T-cell epitopes target targets the Coronaviridae the spike protein Vaccine vaccine candidate vaccine candidates vaccine target virus was used were used Z score [DOI] 10.7717/peerj.9855 PMC 바로가기 [Article Type] Bioinformatics
In Silico Structure-Based Repositioning of Approved Drugs for Spike Glycoprotein S2 Domain Fusion Peptide of SARS-CoV-2: Rationale from Molecular Dynamics and Binding Free Energy CalculationsResearch Article Published on 2020-09-222022-10-29 Journal: mSystems [Category] COVID-19, [키워드] ACE-2 acute respiratory syndrome analyzed angiotensin-converting enzyme 2 antiviral properties attribute binding binding free energy binding site biological systems calculation classical computer-aided drug design coronavirus coronavirus disease COVID-19 direct fusion docking drug Drug discovery Dynamics energy evaluated exhibit Features Free free energy fusion fusion peptide fusion protein Host host cell host cell receptor hydrophobic pocket inferences Interaction mechanism membrane molecular molecular docking molecular dynamics Molecular dynamics simulation molecular mechanics/generalized Born model and solvent accessibility pandemic physiological Protein provide rationale reported repositioning repurposing residue residues S2 domain S2 fusion peptide-containing domain SARS-CoV-2 screened selected selected drug severe acute respiratory syndrome coronavirus 2 shown small molecule Small molecules solvent spike Spike protein statistical the S protein the SARS-CoV-2 Trajectories variables virus were used [DOI] 10.1128/mSystems.00382-20 PMC 바로가기 [Article Type] Research Article
Rapid determination and optimisation of berberine from Himalayan Berberis lycium by soxhlet apparatus using CCD-RSM and its quality control as a potential candidate for COVID-19Short communication Published on 2020-08-132022-10-05 Journal: Natural Product Research [Category] COVID19(2023년), SARS, 치료제, [키워드] Antiviral Asia berberine Berberis Care CCD-RSM condition COVID-19 ethyl alcohol Health highest HPLC investigation methodology plant Quality control Rapid Region risk SARS-CoV-2 shown solvent Soxhlet extraction subtropical treating COVID-19 Vaccine was obtained [DOI] 10.1080/14786419.2020.1806274 [Article Type] Short communication
Physicochemical properties of SARS‐CoV‐2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality controlReview Published on 2020-06-082022-10-31 Journal: Electrophoresis [Category] COVID-19, SARS, [키워드] acute respiratory syndrome adjuvants approach approval average buffer centrifugation competent condition conditions coronavirus COVID‐19 downstream Effects epitope example feasible Formulation immunologically inactivation information knowledge membranes Physicochemical properties Protein Quality control Radiation rigidity SARS‐CoV‐1 SARS‐CoV‐2 SARS‐CoV solvent stability Support susceptibility temperature transfer UV light Vaccine Vaccine development virus virus inactivation [DOI] 10.1002/elps.202000121 PMC 바로가기 [Article Type] Review
The human coronavirus HCoV-229E S-protein structure and receptor bindingResearch Article Published on 2019-10-252022-10-31 Journal: eLife [Category] Coronavirus, [키워드] 229E aminopeptidase N class complex conformational change conserved coronavirus Coronaviruses Cross-species transmission crystal structure electron cryomicroscopy facilitated HCoV-229E host cell membranes hydrophilic immune evasion Interaction membrane fusion plasticity RBD Receptor binding Receptor binding domain S-protein sequence variation solvent specificity Spike protein Structure subunit interface virus X-ray X-ray crystallography [DOI] 10.7554/eLife.51230 PMC 바로가기 [Article Type] Research Article
Sambucus nigra extracts inhibit infectious bronchitis virus at an early point during replicationResearch Article Published on 2014-01-162022-10-28 Journal: BMC veterinary research [Category] Coronavirus, [키워드] Rhodiola rosea Sambucus nigra Anti-viral drugs bronchitis Cell compounds Concentration coronavirus Cytopathic effect cytotoxicity derivative determined different Effect electron microscopy highest IBV infected cell Infection Infectious Bronchitis Virus inhibit magnitude mechanism of action membrane MOI multiplicity of infection Nigella Sativa non-infectious other coronavirus pathogenic plant Plaque assay Prevent protocol quantified reduced Replication Result Rhodiola Safe Sambucus solvent staining suggested supernatant tested tissue transmission electron microscopy treat treated Treatment trypan blue staining vaccination Vero Cell vesicles viral titer virion virus virus inhibition virus titer viruses [DOI] 10.1186/1746-6148-10-24 PMC 바로가기 [Article Type] Research Article
Identification of Residues of SARS-CoV nsp1 That Differentially Affect Inhibition of Gene Expression and Antiviral SignalingResearch Article Published on 2013-04-292022-10-28 Journal: PLoS ONE [Category] Coronavirus, [키워드] activities activity Amino acid analyzed Antiviral antiviral signaling coronavirus Critical drugs drugs targeting Epidemic evade expression Factor greater help Host host gene expression host response identification inhibit inhibition inhibitory inhibitory activity innate immune response interact interferon involved led to mutant Mutation non-structural protein pathway Protein residue residues respiratory SARS-CoV severe Signaling solvent suggested susceptible virus [DOI] 10.1371/journal.pone.0062416 PMC 바로가기 [Article Type] Research Article
Profiling of Substrate Specificity of SARS-CoV 3CL proResearch Article Published on 2010-10-062022-10-28 Journal: PLoS ONE [Category] Coronavirus, [키워드] 3CL pro autocleavage charged residue cleavage Coronaviral correlated demonstrated detected different electrostatic interaction energy transfer finding fluorescent protein found Gln hydrophobic hydrophobic residue in vitro Infection inhibitors Mutagenesis polyprotein Profiling protease required residue residues SARS-CoV sequence solvent specificity Structural properties substitutions substrate variant wild-type β-sheet [DOI] 10.1371/journal.pone.0013197 PMC 바로가기 [Article Type] Research Article