In silico Characterization and Homology Modeling of Histamine Receptors

Zobayer, Nayem; Hossain, Arafat

doi:10.3923/jbs.2018.178.191

Cited by 17 publications

(17 citation statements)

References 22 publications

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“…The additional allowed region and generously allowed region might also contain some percentage of the amino acids of the protein. However, no amino acid should reside within the disallowed region (Sateesh et al, 2010;Laskowski et al, 1993;Zobayer, 2018).…”

Section: D Structure Refinement and Validationmentioning

confidence: 99%

Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2)

et al. 2020

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SARS Coronavirus-2 (SARS-CoV-2) pandemic has become a global issue which has raised the concern of scientific community to design and discover a countermeasure against this deadly virus. So far, the pandemic has caused the death of hundreds of thousands of people upon infection and spreading. To date, no effective vaccine is available which can combat the infection caused by this virus. Therefore, this study was conducted to design possible epitope-based subunit vaccines against the SARS-CoV-2 virus using the approaches of reverse vaccinology and immunoinformatics. Upon continual computational experimentation, three possible vaccine constructs were designed and one vaccine construct was selected as the best vaccine based on molecular docking study which is supposed to effectively act against the SARS-CoV-2. Thereafter, the molecular dynamics simulation and in silico codon adaptation experiments were carried out in order to check biological stability and find effective mass production strategy of the selected vaccine. This study should contribute to uphold the present efforts of the researches to secure a definitive preventative measure against this lethal disease.

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Section: D Structure Refinement and Validationmentioning

confidence: 99%

Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2)

et al. 2020

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show abstract

“…QMEAN scoring function assess the global and per-residue model quality to quantify modeling errors (Waterhouse et al., 2018 ). The predicted structures are verified via ERRAT, RAMPAGE, PROCHECK, ProSA-web (Wiederstein & Sippl, 2007 ), and QMEANBrane web servers (Studer et al., 2014 ; Zobayer & Hossain, 2018 ) as validation and quality assessment are the crucial task for three-dimensional structures (Pražnikar et al., 2019 ). In addition, all model structures are subjected to molecular dynamics simulation by incorporating the membrane environment.…”

Section: Introductionmentioning

confidence: 99%

Structure and dynamics of membrane protein in SARS-CoV-2

Mahtarin

Islam

et al. 2020

Journal of Biomolecular Structure and Dynamics

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“…A few percent of the amino acids of the protein may also occur in the additional region and generously allowed region. However, there should be no amino acid in the unauthorized region (Laskowski et al, n.d.;Sateesh et al, 2010;Zobayer & others, 2019) For further analysis and validation, the 3D protein structures created in the previous step have been re ned. With the help of the Ramachandran Plots, the re ned structures were validated.…”

Section: Methodsmentioning

confidence: 99%

Vaccine Design, Adaptation, and Cloning Design for Multiple Epitope-Based Vaccine Derived From SARS-CoV-2 Surface Glycoprotein (S), Membrane Protein (M) and Envelope Protein (E): In silico approach

Habib

2021

Preprint

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The SARS Coronavirus-2 (SARS-CoV-2) pandemic has become a global epidemic that has increased the scientific community's concern about developing and finding a counteraction against this lethal virus. So far, hundreds of thousands of people have been infected by the pandemic due to contamination and spread. This research was therefore carried out to develop potential epitope-based vaccines against the SARS-CoV-2 virus using reverse vaccinology and immunoinformatics approaches. Three potential vaccine constructs were designed after intensive computational experimentation, and one vaccine model was chosen as the best vaccine based on a molecular docking analysis that is intended to work efficiently against SARS-CoV-2. In order to verify biological stability and find an appropriate mass production technique for the chosen vaccine, molecular dynamics simulation, and silico codon adaptation studies were subsequently carried out. This study should help to maintain current research efforts to secure a definitive preventive measure against this contagious disease.

show abstract

In silico Characterization and Homology Modeling of Histamine Receptors

Cited by 17 publications

References 22 publications

Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2)

Immunoinformatics-guided designing of epitope-based subunit vaccines against the SARS Coronavirus-2 (SARS-CoV-2)

Structure and dynamics of membrane protein in SARS-CoV-2

Vaccine Design, Adaptation, and Cloning Design for Multiple Epitope-Based Vaccine Derived From SARS-CoV-2 Surface Glycoprotein (S), Membrane Protein (M) and Envelope Protein (E): In silico approach

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