Browsing by Author "Narayan, Aditya"

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    In silico methods for the identification of viral-derived small interfering RNAs (vsiRNAs) and their application in plant genomics
    (Springer Nature Publishing AG, 2022) Narayan, Aditya; Zahra, Shafaque; Singh, Ajeet; Kumar, Shailesh
    The current era of high-throughput sequencing (HTS) technology has expedited the detection and diagnosis of viruses and viroids in the living system including plants. HTS data has become vital to study the etiology of the infection caused by both known as well as novel viral elements in planta, and their impact on overall crop health and productivity. Viral-derived small interfering RNAs are generated as a result of defence response by the host via RNAi machinery. They are immensely exploited for performing exhaustive viral investigations in plants using bioinformatics as well as experimental approaches. This chapter briefly presents the basics of virus-derived small interfering RNAs (vsiRNAs) biology in plants and their applications in plant genomics and highlights in silico strategies exploited for virus/viroid detection. It gives a systematic pipeline for vsiRNAs identification using currently available bioinformatics tools and databases. This will surely work as a quick beginner’s recipe for the in silico revelation of plant vsiRNAs as well as virus/viroid diagnosis using high-throughput sequencing data.
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    Protein homology modeling in phytochemical research
    (Springer Nature Publishing AG, 2019) Narayan, Aditya; Singh, Ajeet; Kumar, Shailesh
    The advancements in phytochemical research have offered a number of promising innovations within the field of pharmaceuticals. However, the lack of knowledge related to 3D phytochemical structures has greatly hindered the progress in the field of therapeutic drug discovery and understanding the roles of phytochemicals in biological respects. In recent years, there has been a rapid rise in the number of tools allowing the users to access the modeling methods through a broad spectrum of techniques. In most of the cases, there is a lack of experimental data pertaining to specific structures. However, the most reliable method to obtain structural information construct models is based on the known structural information from homologous proteins. This process is referred to as homology modeling. Advances in homology modeling will provide a number of critical applications in drug design/discovery and is believed to offer a variety of novel research applications with respect to the discovery of novel phytoconstituents. This chapter aims to provide a comprehensive introduction and guide to commonly applied homology modeling tools.