Computational Methodology for Peptide Vaccine Design for Zika Virus: A Bioinformatics Approach

Nandy, Ashesh; Manna, Sourav; Basak, Subhash C.

doi:10.1007/978-1-0716-0389-5_2

Cited by 5 publications

References 30 publications

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Non-standard bioinformatics characterization of SARS-CoV-2

Bielińska-Wąż

Wąż

2021

Computers in Biology and Medicine

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A non-standard bioinformatics method, 4D-Dynamic Representation of DNA/RNA Sequences , aiming at an analysis of the information available in nucleotide databases, has been formulated. The sequences are represented by sets of “material points” in a 4D space - 4D-dynamic graphs. The graphs representing the sequences are treated as “rigid bodies” and characterized by values analogous to the ones used in the classical dynamics. As the graphical representations of the sequences, the projections of the graphs into 2D and 3D spaces are used. The method has been applied to an analysis of the complete genome sequences of the 2019 novel coronavirus. As a result, 2D and 3D classification maps are obtained. The coordinate axes in the maps correspond to the values derived from the exact formulas characterizing the graphs: the coordinates of the centers of mass and the 4D moments of inertia. The points in the maps represent sequences and their coordinates are used as the classifiers. The main result of this work has been derived from the 3D classification maps. The distribution of clusters of points which emerged in these maps, supports the hypothesis that SARS-CoV-2 may have originated in bat and in pangolin. Pilot calculations for Zika virus sequence data prove that the proposed approach is also applicable to a description of time evolution of genome sequences of viruses.

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Non-standard bioinformatics characterization of SARS-CoV-2

Bielińska-Wąż

Wąż

2021

Computers in Biology and Medicine

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Zika virus precursor membrane peptides induce immune response in peripheral blood mononuclear cells

Gupta,

Baranwal,

Chudasama

2024

Human Immunology

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Immunoinformatics Patterns and Characteristic of Epitope-Based Peptide Vaccine candidates against COVID-19

Mustafa

Abdelmoneim

Makhawi

2020

Preprint

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Vaccination as defined by the WHO is “the administration of agent-specific, but safe, antigenic components that in vaccinated individuals can induce protective immunity against the corresponding infectious agent”. Regardless of their debated history, the standard vaccine approaches have been unsuccessful in providing vaccines for numerous infectious organisms. In the recent three decades, an enormous amount of immunological data was retrieved from clinical studies due to the advancement in human genome sequencing. These data are being deposited in databases and numerous scientific literature. The development of several bioinformatics tools to analyze this rapidly increasing immunological databank has given rise to the field of immunoinformatics. This approach allows the selection of immunogenic residues from the pathogen genomes. The ideal residues could be industrialized as vaccine candidates to provide protective immune responses in the hosts. This methodology will significantly decrease the time and cost needed for the vaccine development. This review focus on published articles that proposed as vaccine candidates through immunoinformatics analysis. The reviewed Published immunoinformatics studies provided vaccine peptide candidates against SARS-COV-2, which is based on functional and non functional immunogenic proteins like open reading frame , spike protein, envelope protein and membranous protein .All of which are designed by unique strategies like reverse vaccinology . Spike protein was the most common used target with different suggeststed B and T cell peptides due to the difference in methodology between the findings.

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Computational Methodology for Peptide Vaccine Design for Zika Virus: A Bioinformatics Approach

Cited by 5 publications

References 30 publications

Non-standard bioinformatics characterization of SARS-CoV-2

Non-standard bioinformatics characterization of SARS-CoV-2

Zika virus precursor membrane peptides induce immune response in peripheral blood mononuclear cells

Immunoinformatics Patterns and Characteristic of Epitope-Based Peptide Vaccine candidates against COVID-19

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