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Rajdeep Poddar

Bio: Rajdeep Poddar is an academic researcher. The author has contributed to research in topics: Proteome & Genomics. The author has an hindex of 2, co-authored 2 publications receiving 42 citations.
Topics: Proteome, Genomics, Xanthine, Genome project

Papers
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Journal ArticleDOI
TL;DR: This review enlist various methods linking annotation to structural and functional prediction of HPs that assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery, and screening.
Abstract: Hypothetical Proteins are the proteins that are predicted to be expressed from an open reading frame (ORF), constituting a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein and their interactions. In this review we have enlisted various methods. Annotation linked to structural and functional prediction of hypothetical proteins assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery and screening. Mass spectrometry is an analytical technique for validating protein characterisation. Matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS) is an efficient analytical method. Microarrays and Protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells and tissues and even whole organism. Next generation sequencing technology accelerates multiple areas of genomics research.

61 citations

Book ChapterDOI
01 Jan 2014
TL;DR: This mini review focuses on the molecular modeling of xanthine derivatives which, in the recent past, has proved to be a promising avenue for structure-based methods of target identification.
Abstract: Xanthines and its derivatives are a group of alkaloids which are well represented in plants The xanthine analogs play a key role as adenosine receptors and calcium release channels and therefore can be used as behavioral stimulants Various such stimulants in the form of bronchodilators, diuretics, natriuretics, analgesic adjuvants, and lipolytics are in use This mini review focuses on the molecular modeling of xanthine derivatives which, in the recent past, has proved to be a promising avenue for structure-based methods of target identification

5 citations


Cited by
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Journal ArticleDOI
01 Oct 2018-Heliyon
TL;DR: In this paper, a review summarizes the available knowledge of xanthine based drugs development along with exploring new Xanthine led chemical synthesis path for bringing diversification in xanthines based research.

65 citations

Journal ArticleDOI
TL;DR: Physicochemical analyses of the granules indicated that extracellular structural matrix proteins likely have β-sheet dominated secondary structures, and alkaline and ionic liquid extractions were compared in terms of the proteins they extracted from different "Candidatus Brocadia" cultures.

59 citations

01 Jan 2018
TL;DR: The main objective of this review is to explore the immense potential of xanthine as scaffold in drug development and the probable solution to fill existing lacuna.

47 citations

Journal ArticleDOI
01 Mar 2020
TL;DR: The analysis of bacterial genomes from the Genome Taxonomy Database revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively, highlighting the disparity in annotation coverage.
Abstract: Although gene-finding in bacterial genomes is relatively straightforward, the automated assignment of gene function is still challenging, resulting in a vast quantity of hypothetical sequences of unknown function. But how prevalent are hypothetical sequences across bacteria, what proportion of genes in different bacterial genomes remain unannotated, and what factors affect annotation completeness? To address these questions, we surveyed over 27 000 bacterial genomes from the Genome Taxonomy Database, and measured genome annotation completeness as a function of annotation method, taxonomy, genome size, 'research bias' and publication date. Our analysis revealed that 52 and 79 % of the average bacterial proteome could be functionally annotated based on protein and domain-based homology searches, respectively. Annotation coverage using protein homology search varied significantly from as low as 14 % in some species to as high as 98 % in others. We found that taxonomy is a major factor influencing annotation completeness, with distinct trends observed across the microbial tree (e.g. the lowest level of completeness was found in the Patescibacteria lineage). Most lineages showed a significant association between genome size and annotation incompleteness, likely reflecting a greater degree of uncharacterized sequences in 'accessory' proteomes than in 'core' proteomes. Finally, research bias, as measured by publication volume, was also an important factor influencing genome annotation completeness, with early model organisms showing high completeness levels relative to other genomes in their own taxonomic lineages. Our work highlights the disparity in annotation coverage across the bacterial tree of life and emphasizes a need for more experimental characterization of accessory proteomes as well as understudied lineages.

46 citations

Journal ArticleDOI
TL;DR: Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide and is involved in nosocomial infections.

41 citations